gebhart/patrepeval huggingface dataset:
PCR-Based Serotyping of Streptococcus pneumoniae from Culture-Negative Specimens: Novel Primers for Detection of Serotypes within Serogroup 18 (2016)

Six multiplex-compatible PCR primers were designed to distinguish Streptococcus pneumoniae serotypes within serogroup 18 from culturable/nonculturable pneumococcal specimens, with no cross-reactivity with other serotypes and respiratory organisms. These primers will aid in the generation of better data on vaccine/nonvaccine serotypes in invasive and carriage pneumococcal surveillance and contribute to future vaccine formulation and impact studies.
Chemical composition and antimicrobial activity of essential oil from cones of Pinus koraiensis. (2008)

The essential oil from the cones of Pinus koraiensis was prepared after removing the seeds, and its chemical composition analyzed using gas chromatography-mass spectrometry (GC-MS). Hydrodistillation of the P. koraiensis cones yielded 1.07% (v/w) of essential oil, which was almost three times the amount of essential oil extracted from the needles of the same plant. Moreover, the antimicrobial activities of the oil against the growth of Gram-positive bacteria, Gram-negative bacteria, and fungi were evaluated using the agar disc diffusion method and broth microdilution method. Eighty-seven components, comprising about 96.8% of the total oil, were identified. The most abundant oil components were limonene (27.90%), alpha-pinene (23.89%), beta-pinene (12.02%), 3-carene (4.95%), beta-myrcene (4.53%), isolongifolene (3.35%), (-)-bornyl acetate (2.02%), caryophyllene (1.71%), and camphene (1.54%). The essential oil was confirmed to have significant antimicrobial activities, especially against pathogenic fungal strains such as Candida glabrata YFCC 062 and Cryptococcus neoformans B 42419. Therefore, the present results indicate that the essential oil from the cones of Pinus koraiensis can be used in various ways as a nontoxic and environmentally friendly disinfectant.
Molecular cloning and chromosomal localisation of the human homologue of a receptor related to tyrosine kinases (RYK). (1993)

A cDNA encoding the human homologue of mouse RYK (related to receptor tyrosine kinases) has been cloned from an interleukin 1 (IL-1)-stimulated human hepatoma cDNA library by cross-species hybridization using the mouse RYK cDNA as a probe. The sequence of the 3067-bp cDNA clone encoding human RYK predicts a transmembrane protein with a cytoplasmic domain that contains the consensus sequences (subdomains I-XI) of the protein tyrosine kinase (PTK) family. The highly conserved motif -D-F-G- (subdomain VII) of the catalytic domain of other receptor-type tyrosine kinases is altered to -D-N-A- in human RYK. In addition, a number of other changes were found in the ATP binding site (subdomains I and II) and the motif [-I-H-R-D-L-A-A-R-N-] found in subdomain VI. Comparison of the human and mouse RYK sequences shows a 92% conservation at the nucleotide level and 97% at the amino acid level. There was no significant homology between the extracellular domain of RYK and the other families of receptor tyrosine kinases described to date. RYK therefore appears to define a new subclass of receptor-type tyrosine kinases whose structure has remained highly conserved across species.
Apoptosis-induced Cleavage of β-Catenin by Caspase-3 Results in Proteolytic Fragments with Reduced Transactivation Potential (2000)

Beta-catenin is a member of the Armadillo repeat protein family with a dual cellular function as a component of both the adherens junction complex and the Wnt/wingless signaling pathway. Here we show that beta-catenin is proteolytically cleaved during anoikis and staurosporine-induced apoptosis. Cleavage of beta-catenin was found to be caspase-dependent. Five cleavage products of beta-catenin were identified in vivo and after in vitro cleavage by caspase-3. Amino acid sequencing and mass spectrometry analysis indicated two caspase-3 cleavage sites at the C terminus and three further sites at the N terminus, whereas the central Armadillo repeat region remained unaffected. All beta-catenin cleavage products were still able to associate with E-cadherin and alpha-catenin and were found to be enriched in the cytoplasm. Functional analysis revealed that beta-catenin deletion constructs resembling the observed proteolytic fragments show a strongly reduced transcription activation potential when analyzed in gene reporter assays. We therefore conclude that an important role of the beta-catenin cleavage during apoptosis is the removal of its transcription activation domains to prevent its transcription activation potential.
The Significance of CD5<sup>+</sup>B Cells in Rheumatic Diseases (1988)

The presence of autoantibodies in rheumatoid arthritis (RA) and primary Sjögren' syndrome (SS) is a feature of these diseases. Because of the probable role of autoantibodies in the pathogenesis of RA and primary SS, the study of the origin and regulation of B lymphocytes producing autoantibodies is of special importance. In mice, B lymphocytes can be divided into two populations of distinct lineages, the conventional bone marrow-derived B subset and the self-renewing peripheral subset. B lymphocytes of the latter express an antigen initially described as T cell specific, the Ly-1 or CD5 antigen. In human, such CD5+B cells are found in foetal lymphoid tissue but their frequency diminishes in adult life. We have found a significant increase in CD5+B cells in the peripheral blood of patients with RA and primary SS, and a small family study of relatives of two RA patients suggests that such 'high phenotype' could be a genetic trait. Furthermore, CD5+B cells appear enriched in autoantibody-producing cells since they produce IgM-rheumatoid and other autoantibodies when suitably activated in vitro. Our current hypothesis is that persistence of high numbers of CD5+B cells in adulthood may predispose to chronic inflammatory arthritis due to the reactivity of the antigen receptor of these cells with a variety of autoantigens in the joint. Such reactivity would allow an autoimmune reactions causing the perpetuation of chronic inflammation at the disease site.
Fast and unbiased purification of RNA-protein complexes after UV cross-linking (2019)

Post-transcriptional regulation of gene expression in cells is facilitated by formation of RNA-protein complexes (RNPs). While many methods to study eukaryotic (m)RNPs rely on purification of polyadenylated RNA, other important regulatory RNA classes or bacterial mRNA could not be investigated at the same depth. To overcome this limitation, we developed Phenol Toluol extraction (PTex), a novel and unbiased method for the purification of UV cross-linked RNPs in living cells. PTex is a fast (2-3 h) and simple protocol. The purification principle is solely based on physicochemical properties of cross-linked RNPs, enabling us to interrogate RNA-protein interactions system-wide and beyond poly(A) RNA from a variety of species and source material. Here, we are presenting an introduction of the underlying separation principles and give a detailed discussion of the individual steps as well as incorporation of PTex in high-throughput pipelines.
Minimizing Morbidity of Organ Donation: Analysis of Factors for Perioperative Complications After Living-Donor Nephrectomy in the United States (2008)

The inclusion of donors with tobacco abuse, obesity, and age >50 increases complications; however, the risk of major morbidity is small. Use of administrative data represents an important tool to facilitate the reconciliation of an increased need for organ donors with the concern for donor safety.
Adenosine-Induced Transient Cardiac Asystole Enhances Precise Deployment of Stent-Grafts in the Thoracic or Abdominal Aorta (1996)

Pharmacologically induced transient asystole appears to be a safe maneuver to preclude endograft movement by systolic blood flow. The technique permits precise placement of balloon-expandable stent-grafts and is applicable to self-expanding devices as well. Interventionists may wish to incorporate adenosine-induced asystole into their aortic aneurysm exclusion procedures.
Ocular Gene Transfer of Active TGF-β Induces Changes in Anterior Segment Morphology and Elevated IOP in Rats (2010)

Purpose. Transforming growth factor beta (TGF-beta) is known to play a crucial role in wound healing and fibrotic tissue remodeling. A large body of evidence suggests a role for this cytokine in the pathogenesis of glaucoma; however, the mechanisms by which it affects anterior segment morphology are not well understood. Therefore, the purpose of this study was to examine the effects of TGF-beta overexpression on anterior segment morphology and subsequent effects on intraocular pressure. Methods. Adenoviral gene transfer was used to deliver active TGF-beta1 to the rat eye. Measurements of intraocular pressure were taken with a tonometer on days 0, 14, 21, and 29. Histologic analysis was undertaken to examine anterior segment morphology, and markers of matrix deposition and fibrosis were used. Results. Gene transfer of TGF-beta in the anterior segment resulted in the formation of peripheral anterior synechiae (PAS), which consisted of a fibroproliferative region of corneal endothelial cells, matrix accumulation, and decrease in trabecular meshwork expression of alpha-smooth muscle actin. These features were accompanied by ocular hypertension. Conclusions. Gene transfer of TGF-beta into the anterior segment induces aberrant PAS associated with the transition of corneal endothelial cells and subsequent matrix deposition. These features are highly reminiscent of human iridocorneal endothelial (ICE) syndrome. Gene transfer of TGF-beta can, therefore, be used to induce anatomic changes in the anterior segment in a rodent model that result in ocular hypertension.
One-pot synthesis of PtRu nanodendrites as efficient catalysts for methanol oxidation reaction (2016)

Bimetallic Pt-based nanodendrites are of particular interest in various catalytic applications due to their high surface areas and low densities. Herein, we provide a facile method for one-pot synthesis of PtRu nanodendrites via the co-reduction of Pt and Ru precursors in oleylamine by H<sub>2</sub>. The as-fabricated PtRu nanodendrites exhibit superior catalytic activity and durability compared with PtRu nanocrystals (NCs), synthesized under the same reaction conditions, and the commercial Pt/C catalyst towards the methanol oxidation reaction (MOR).
Synthesis and Nematicidal Activities of 1,2,3-Benzotriazin-4-one Derivatives against <i>Meloidogyne incognita</i> (2015)

A series of novel 1,2,3-benzotriazin-4-one derivatives were synthesized by the reaction of 3-bromoalkyl-1,2,3-benzotriazin-4-ones with potassium salt of 2-cyanoimino-4-oxothiazolidine in the presence of potassium iodide. Nematicidal assays in vivo showed that some of them exhibited good control efficacy against the cucumber root-knot nematode disease caused by Meloidogyne incognita, up to 100% at the concentration of 10.0 mg L(-1), which indicated that 1,2,3-benzotriazin-4-one derivatives might be potential for novel promising nematicides. The nematicidal activity was influenced by the combination of substituent type, substituted position, and linker length in the molecule. The inhibition rate data at the concentrations of 5.0 and 1.0 mg L(-1) for the compounds with high inhibitory activities were also provided. When tested in vitro, none of them showed direct inhibition against M. incognita. The investigation of a significant difference between in vivo and in vitro data is in progress.
Fluxgate magnetometers for outer planets exploration (1974)

The exploration of the interplanetary medium and the magnetospheres of the outer planets requires the implementation of magnetic field measuring instrumentation with wide dynamic range, high stability, and reliability. The fluxgate magnetometers developed for the Pioneer 11 and Mariner-Jupiter-Saturn missions are presented. These instruments cover the range of .01 nT to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 \times 10^{6}</tex> nT with optimum performance characteristics and low power consumption.
Affinity Purification of a Human RNA Polymerase II Complex Using Monoclonal Antibodies against Transcription Factor IIF (1997)

Five different monoclonal antibodies that immunoreact with RAP74, the large subunit of general transcription factor (TF) IIF, were produced and characterized. Using one of these antibodies, an affinity purification procedure was devised to isolate a human RNA polymerase II complex. This procedure is fast, simple, and reproducible and does not require extensive purification. The RNA polymerase II complex isolated using this procedure contains SRB (suppressor of RNA polymerase B) polypeptides, transcription factors IIE and IIF, limiting amounts of TFIIH, and the TATA-binding protein, but was devoid of TFIIB.
Hierarchical Pore Structure and Wetting Properties of Single-Wall Carbon Nanotube Fibers (2003)

We show that single-wall carbon nanotube (SWNT) fibers produced by the particle-coagulation spinning process possess a well-developed hierarchical skin−core structure. Primary SWNTs are organized in bundles that are 10−30 nm in diameter. The nanotube bundles form elementary filaments, which constitute the fiber skin, and a highly porous nanofelt, which fills the fiber core. The elementary filaments of ∼0.2−2 μm diameter are well aligned along the fiber axis and densely packed. The hierarchical pore structure organization determines unique wetting and sorption properties of SWNT fibers. Experiments with capillary condensation and droplet absorption of wetting fluids agree with the proposed skin−core model and can be used for pore structure characterization. The well-developed porosity and high surface area in conjunction with controllable electrical and mechanical functionalities make the SWNT fibers attractive materials for nanotechnologies, where wetting and sorption properties play an important role.
Purification and structure elucidation of the <i>N</i>‐acetylbacillosamine‐containing polysaccharide from <i>Bacillus licheniformis</i> ATCC 9945 (2001)

The exopolysaccharide of Bacillus licheniformis ATCC 9945 (formerly B. subtilis ATCC 9945) contains among other glycoses 4-acetamido-2-amino-2,4,6-trideoxy-D-glucose, termed N-acetylbacillosamine (Bac2N4NAc). A similar diamino glycose, 2-acetamido-4-amino-2,4,6-trideoxy-D-glucose, was found in a surface layer (S-layer) glycoprotein preparation of Clostridium symbiosum HB25. Electron microscopic studies, however, showed that B. licheniformis ATCC 9945 is not covered with an S-layer lattice, indicating that the N-acetylbacillosamine present in that organism might be a constituent of a cell wall-associated polymer. For elucidation of the structure of the N-acetylbacillosamine-containing polysaccharide, it was purified from a trichloroacetic acid extract of B. licheniformis ATCC 9945 cells. Using different hydrolysis protocols and a hydrolysate of the S-layer glycoprotein preparation from C. symbiosum HB25 as reference, the purified polysaccharide was found to contain 2,4-diamino-2,4,6-trideoxy-glucose, 2-acetamido-2-deoxy-glucose, 2-acetamido-2-deoxy-galactose and galactose in a molar ratio of 1 : 1 : 1 : 2. One- and two-dimensional NMR spectroscopy, including 800 MHz proton magnetic resonance measurements, in combination with chemical modification and degradation experiments, revealed that the polysaccharide consists of identical pyruvylated pentasaccharide repeating units with the structure: [-->3)-[(S)Py-(3,4)-beta-D-Galp-(1-->6)]-alpha-D-GlcpNAc-(1-->3)-beta-D-Bacp2N4NAc-(1-->3)-[(S)Py-(3,4)-beta-D-Galp-(1-->6)]-beta-D-GalpNAc-(1-->](n)
Automatic Document Logo Detection (2007)

Automatic logo detection and recognition continues to be of great interest to the document retrieval community as it enables effective identification of the source of a document. In this paper, we propose a new approach to logo detection and extraction in document images that robustly classifies and precisely localizes logos using a boosting strategy across multiple image scales. At a coarse scale, a trained Fisher classifier performs initial classification using features from document context and connected components. Each logo candidate region is further classified at successively finer scales by a cascade of simple classifiers, which allows false alarms to be discarded and the detected region to be refined. Our approach is segmentation free and lay-out independent. We define a meaningful evaluation metric to measure the quality of logo detection using labeled groundtruth. We demonstrate the effectiveness of our approach using a large collection of real-world documents.
Characterization of single heat-activated Bacillus spores using laser tweezers  Raman spectroscopy (2009)

Heat activation of dormant bacterial spores is a short treatment at a sublethal temperature that potentiates and synchronizes spore germination. In this paper, laser tweezers Raman spectroscopy (LTRS) was used to study the heat activation of single spores of Bacillus cereus and Bacillus subtilis. We measured the Raman spectra of single spores without treatment, during heat activation at 65 degrees C (B. cereus) or 70 degrees C (B. subtilis), and following heat activation and cooling to 25 degrees C. Principle component analysis (PCA) was applied to discriminate among the three groups of spores based on their Raman spectra. The results indicated that: (1) there are large changes in the Raman bands of Ca-DPA and protein for both B. cereus and B. subtilis spores during heat activation, indicative of changes in spore core state and partial protein denaturation at the heat activation temperatures; (2) these spectral changes become smaller once the heated spores are cooled, consistent with heat activation being reversible; (3) minor spectral differences between untreated and heat-activated and cooled spores can be discriminated by PCA based on non-polarized and polarized Raman spectra; and (4) analysis based on polarized Raman spectra reveals that partial denaturation of protein during heat activation is mainly observed in the vertically polarized component.
Parallel acquisition of fluorescence decay using array detectors (1990)

Frequency domain fluorometry provides an alternative method for the recording of fluorescence decay kinetics (1), The major advantages of this method are the time resolution and the fast measurement of lifetime values. There are several systems, where a change in lifetime occurs across the emission band. These systems include heterogeneous ground state systems, where species emit at different wavelengths; excited state reactions, with products emitting at different parts of the spectrum; and dipolar relaxation processes, where the emission spectra change with time. To characterize the decay of the systems, it is necessary to collect the emission decay at several wavelengths. Generally, this process is obtained by successive measurements using a monochromator or a series of bandpass filters. For steady-state spectra, optical multichannel analyzers (OMA) are available, which can collect the entire emission spectra at once. By gating the image intensifier, used with some of these analyzers, it is possible to obtain time windows of the order of a few nanoseconds (2), This time resolution is inadequate for most of the fluorescence substances. We have developed a new method based of frequency domain fluorometry which extends the time resolution of an OMA to the picosecond region. The entire emission decay is collected in a few seconds and the lifetime information across the entire emission band is analyzed. The same method can be applied to other array detectors such as TV and CCD cameras used in fluorescence microscopy (3).
Hydrodynamics of the rupture of thin liquid films (1990)

Experiments on the rupture of a thin spherical liquid film – formed from a solution of surfactant – are reported. The mean film thickness, prior to rupture, was measured by an electrical conductivity method: initial film thicknesses were of order 0.3–0.9 μm. For an unruptured film, drainage due to gravity reduced the film thickness; the films ruptured naturally at a thickness of order 0.05–0.09 μm. When the spherical film was punctured by a needle, a hole was formed, which grew rapidly, bounded by a liquid rim. As the rim moved, it collected the liquid from the film; but the rim was itself unstable, generating droplets continuously. The rim velocity, of order 10 m/s, was measured by cine photography at 2000 frames/s. Measured rim velocities compared well with a simple theoretical result derived from either (i) a force balance on the rim or (ii) an energy balance, which demonstrates that there is continuous energy dissipation due to collision between the moving rim and the elements of the stationary film. When the moving rim had swept up the whole spherical film, much of the rim had disintegrated into droplets, but the remaining rim finally converged to give an ‘implosion’ generating more droplets. These droplets, together with those generated by fragmentation of the rim in flight, were collected: their number, of order 10 4 , was measured by an image analyser, which also measured mean droplet size, of order 10 2 μm. The total droplet area was a few per cent of the area of the original spherical film.
Presentation and Formal Verification of a Family of Protocols for Latency Insensitive Design (2005)

With increasing clock frequencies in the gigahertz ranges, the distance signals travel during one clock cycle decreases, making a synchronous clock routing throughout the chip impossible. Therefore, interconnect latency needs to be tolerated, and in IP based design various synchronous logic blocks need to be connected via long interconnects that have communication delays of multiple clock cycles. Sometimes two communicating IPs also belong to different clock domains, making their interaction difficult to implement. Latency insensitive protocols were introduced for cases when the interconnect delay was the main concern but the IPs were under same clock domain. Here we generalize the issue of solving the problem of long interconnects in between IPs for a single-clock domain as well as for a multi-clock domain. We also use a formal verification strategy for making sure that as we gradually refine our protocol, we do not become functionally inequivalent to the original synchronous reference design. Presentation and Formal Verification of a Family of Protocols for Latency Insensitive Design Syed Suhaib, David Berner, Deepak Mathaikutty, Jean-Pierre Talpin, Sandeep Shukla {ssuhaib,damathai,shukla}@vt.edu {david.berner,talpin}@irisa.fr Presentation and Formal Verification of a Family of Protocols for Latency Insensitive Design Syed Suhaib, David Berner, Deepak Mathaikutty, Jean-Pierre Talpin, Sandeep Kumar Shukla Virgina Tech, USA INRIA, France {ssuhaib,damathai,shukla}@vt.edu {dberner,talpin}@irisa.fr