gebhart/patrepeval huggingface dataset:
Evaluation of the Cornell-Wisconsin centrifugal flotation technique for recovering trichostrongylid eggs from bovine feces. (1982)

Several variables in the Cornell-Wisconsin centrifugal flotation technique were studied using helminthologically sterile bovine feces to which known numbers of Haemonchus contortus eggs had been added. Neither mode of mixing (levigation versus conventional), volume (15-60 mL) of water used for making the feces water suspension nor specific gravity (1.20-1.33) of the sucrose flotation solution affected egg recovery. Optimal times for centrifugation at 264 x g of first the feces water and then the feces sucrose suspension were three and five minutes respectively. Under these conditions 62.6% of the eggs were recoverable and there was a linear relationship between the number of eggs recovered and those added to the feces. About 30% of the unrecovered eggs were found in the fecal debris retained on the strainer. About 5% of the unrecovered eggs were found in the supernatant discarded after the feces water centrifugation and also in the matrix of the viscous sucrose solution. Addition of the detergent Triton X-100 caused a decrease in egg recovery. False negatives were not encountered between 3 to 70 epg; at 1.44 epg there was only one in 14 samples. Optimum procedures for the technique are presented.
Partially labeled classification with Markov random walks (2001)

To classify a large number of unlabeled examples we combine a limited number of labeled examples with a Markov random walk representation over the unlabeled examples. The random walk representation exploits any low dimensional structure in the data in a robust, probabilistic manner. We develop and compare several estimation criteria/algorithms suited to this representation. This includes in particular multi-way classification with an average margin criterion which permits a closed form solution. The time scale of the random walk regularizes the representation and can be set through a margin-based criterion favoring unambiguous classification. We also extend this basic regularization by adapting time scales for individual examples. We demonstrate the approach on synthetic examples and on text classification problems.
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource (2004)

The Poxvirus Bioinformatics Resource Center (PBRC) has been established to provide informational and analytical resources to the scientific community to aid research directed at providing a better understanding of the Poxviridae family of viruses. The PBRC was specifically established as the result of the concern that variola virus, the causative agent of smallpox, as well as related viruses, might be utilized as biological weapons. In addition, the PBRC supports research on poxviruses that might be considered new and emerging infectious agents such as monkeypox virus. The PBRC consists of a relational database and web application that supports the data storage, annotation, analysis and information exchange goals of the project. The current release consists of over 35 complete genomic sequences of various genera, species and strains of viruses from the Poxviridae family. Sequence and annotation information for these viruses has been obtained from sequences publicly available from GenBank as well as sequences not yet deposited in GenBank that have been obtained from ongoing sequencing projects. In addition to sequence data, the PBRC provides comprehensive annotation and curation of virus genes; analytical tools to aid in the understanding of the available sequence data, including tools for the comparative analysis of different virus isolates; and visualization tools to help better display the results of various analyses. The PBRC represents the initial development of what will become a more comprehensive Viral Bioinformatics Resource Center for Biodefense that will be one of the National Institute of Allergy and Infectious Diseases' 'Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases'. The PBRC website is available at http://www.poxvirus.org.
The role of protein kinase C isozymes in TNF-α-induced cytotoxicity to a rat intestinal epithelial cell line (2001)

Tumor necrosis factor (TNF)-alpha can induce cytotoxicity and apoptosis in a number of cell types and has been implicated in the regulation of many inflammatory processes. It has been suggested that protein kinase C (PKC) is one of the intracellular mediators of the actions of TNF-alpha. In the present study, the role of PKC isoforms in TNF-alpha-mediated cytotoxicity and apoptosis in intestinal cells was investigated using the rat epithelial cell line, IEC-18. Cells were incubated with TNF-alpha in the presence or absence of the transcription inhibitor actinomycin D (AMD). The extent of cell damage was enhanced when AMD was added to incubation medium, suggesting that new protein synthesis plays a role in the cytotoxic action of TNF. TNF-alpha also induced the translocation of PKC-alpha, -delta, and -epsilon from cytosol to the membrane fraction of the intestinal cells. Furthermore, the cytotoxic and apoptotic effects of TNF were reduced by pretreating the cells with the PKC-epsilon translocation inhibitor, PKC-epsilonV1-2. In contrast, although cells incubated with the phorbol ester phorbol 12-myristate 13-acetate (PMA) also displayed an increase in cell injury, the extent of cytotoxicity and apoptosis was not enhanced by AMD. Furthermore, PMA-induced cell damage was reduced by rottlerin, a PKC-delta inhibitor. Caspase-3, an enzyme implicated in the mediation of apoptosis, was activated in cells in response to either TNF-alpha or PMA stimulation, and its effects on this activity were reduced by selective inhibition of PKC-epsilon and -delta, respectively. Furthermore, inhibition of caspase-3 activity reduced apoptosis. These data suggest that activation of selective PKC isoforms mediate the effects of TNF-alpha on intestinal epithelial cell injury.
Selective Proteasomal Degradation of the B′β Subunit of Protein Phosphatase 2A by the E3 Ubiquitin Ligase Adaptor Kelch-like 15 (2012)

Protein phosphatase 2A (PP2A), a ubiquitous and pleiotropic regulator of intracellular signaling, is composed of a core dimer (AC) bound to a variable (B) regulatory subunit. PP2A is an enzyme family of dozens of heterotrimers with different subcellular locations and cellular substrates dictated by the B subunit. B'β is a brain-specific PP2A regulatory subunit that mediates dephosphorylation of Ca(2+)/calmodulin-dependent protein kinase II and tyrosine hydroxylase. Unbiased proteomic screens for B'β interactors identified Cullin3 (Cul3), a scaffolding component of E3 ubiquitin ligase complexes, and the previously uncharacterized Kelch-like 15 (KLHL15). KLHL15 is one of ∼40 Kelch-like proteins, many of which have been identified as adaptors for the recruitment of substrates to Cul3-based E3 ubiquitin ligases. Here, we report that KLHL15-Cul3 specifically targets B'β to promote turnover of the PP2A subunit by ubiquitylation and proteasomal degradation. Comparison of KLHL15 and B'β tissue expression profiles suggests that the E3 ligase adaptor contributes to selective expression of the PP2A/B'β holoenzyme in the brain. We mapped KLHL15 residues critical for homodimerization as well as interaction with Cul3 and B'β. Explaining PP2A subunit selectivity, the divergent N terminus of B'β was found necessary and sufficient for KLHL15-mediated degradation, with Tyr-52 having an obligatory role. Although KLHL15 can interact with the PP2A/B'β heterotrimer, it only degrades B'β, thus promoting exchange with other regulatory subunits. E3 ligase adaptor-mediated control of PP2A holoenzyme composition thereby adds another layer of regulation to cellular dephosphorylation events.
Cloning and molecular analysis of the Salmonella enterica ansP gene, encoding an L-asparagine permease (1995)

A gene (ansP), which encodes an L-asparagine permease, has been isolated from a cosmid library of Salmonella enterica during screening for recombinant clones which encode L-asparaginase. Nucleotide sequence analysis reveals that the gene product is a polypeptide of 497 amino acid residues, containing 12 putative transmembrane segments. The calculated molecular mass is 54 kDa, although maxicell analysis by SDS-PAGE gave an apparent molecular mass of 37 kDa. Comparison of the deduced amino acid sequence with sequence databases showed significant homology with a family of basic and aromatic amino acid permeases. Strains containing the cloned ansP gene demonstrated a many-fold increase in L-asparagine uptake in comparison with control strains.
Active photonic lattices: lasers for watt-range coherent-power generation (2002)

Active photonic lattices (APLs) of large index step have been used, as early as 1988, for effective lateral-mode control in large-aperture (100 microns) high-power coherent devices. Photonic-bandpass (PBP) structures relying on long-range resonant leaky-wave coupling, so called ROW arrays, have allowed stable, near-diffraction-limited beam operation to powers as high as 1.6W CW and 10W peak pulsed. Photonic-bandgap (PBG) structures with a built-in lattice defect, so called ARROW lasers, have provided up to 0.5W peak-pulsed stable, single-mode power and hold the potential for 1W CW reliable single-mode operation from apertures ~10 microns wide. The solution for high-efficiency surface emission, from 2nd-order DFB/DBR lasers, in an orthonormal, single-lobe beam pattern was found in 2000. Recently, single-lobe and single-mode operation in a diffraction-limited beam orthonormal to the chip surface was demonstrated from 1.5mm-long DFB/DBR ridge-guide lasers. That opens the way for the realization of 2-D surface-emitting, 2nd-order APLs for the stable generation of watts of CW single-lobe, single-mode power from large 2-D apertures, as well as scalability of such devices at the wafer level.
Characterization of polyclonal and monoclonal anti-taxol antibodies and measurement of taxol in serum. (1993)

Anti-taxol antibodies were generated in the rabbit using a taxol-bovine serum albumin conjugate prepared from 2'-succinyltaxol using a mixed anhydride procedure. Immunization with 2'-succinyltaxol-bovine serum albumin gave rise to polyclonal anti-taxol antibodies. By a radioimmunoassay using [3H]taxol, a standard curve gave a 50% inhibitory concentration of 1.0 nM. Taxol levels in human serum could be measured, with the lower limit of detection and measurement being 0.1 nM or 0.085 ng/ml. Two mouse monoclonal anti-taxol antibodies were isolated by immunizing BALB/c mice with the same antigen. One was an immunoglobulin G1 (69E4A8E) and the other was immunoglobulin M (29B7B3C). The specificity of these antibodies was determined by a competitive enzyme-linked immunosorbent assay with taxol and 10 different related derivatives and analogues. 29B7B3C had higher binding affinities for biologically active derivatives and markedly lower affinities for inactive derivatives; i.e., the specificity was consistent with the results of tubulin disassembly and cytotoxicity studies using the same taxol derivatives, making it suitable for screening for taxol or taxol-like compounds in extracts of natural products. 69E4A8E recognized the benzamidocarbamyl group at the C-3' position of taxol and had a lower affinity for other active compounds with different substitutions. Taxol levels in human serum could be detected and measured by 69E4A8E using a competitive enzyme-linked immunosorbent assay. The lower limit of measurement was about 50 nM or approximately 42 ng/ml. Similar measurements could be made by radioimmunoassay.
Silver-Coated Endotracheal Tubes and Incidence of Ventilator-Associated Pneumonia (2008)

clinicaltrials.gov Identifier: NCT00148642.
Internalization and processing of transferrin and the transferrin receptor in human carcinoma A431 cells. (1983)

The binding and subsequent intracellular processing of transferrin and transferrin receptors was studied in A431 cells using 125I-transferrin and a monoclonal antibody to the receptor (ATR) labeled with 125I and gold colloid. Using 125I-transferrin we have shown that, whereas at 37 degrees C uptake proceeded linearly for up to 60 min, most of the ligand that was bound was internalized and then rapidly returned to the incubation medium undegraded. At 37 degrees C, the intracellular half-life of the most rapidly recycled transferrin was 7.5 min. 125I-ATR displayed the same kinetics of uptake but following its internalization at 37 degrees C, it was partially degraded. At 22 degrees C and below, the intracellular degradation of 125I-ATR was selectively inhibited and as a result it accumulated intracellularly. Electron microscopy of conventional thin sections and of whole-cell mounts was used to follow the uptake and processing of transferrin receptors labeled with ATR-gold colloid complexes. Using a pulse-chase protocol, the intracellular pathway followed by internalized ATR gold-receptor complexes was outlined in detail. Within 5 min at 22 degrees C the internalized complexes were transferred from coated pits on the cell surface to a system of narrow, branching cisternae within the peripheral cytoplasm. By 15 min they reached larger, more dilated elements that, in thin section, appeared as irregular profiles containing small (30-50-nm diam) vesicles. By 30 min, the gold complexes were located predominantly within typical spherical multivesicular bodies lying in the peripheral cytoplasm, and by 40-60 min, they reached a system of cisternal and multivesicular body elements in the juxtanuclear area. At 22 degrees C, no other compartments became labeled but if they were warmed to 37 degrees C the gold complexes were transferred to lysosome-like elements. Extracting ATR-gold complexes with Triton X after a 30-min chase at 22 degrees C and purifying them on Sepharose-transferrin indicated that the internalized complexes remained bound to the transferrin receptor during their intracellular processing.
Hypertension 1986 (1986)

PreviewPreviewWith changing definitions of hypertension, the number of candidates for treatment has expanded greatly and the physician is continually faced with the questions of whether and how to treat the condition. This article reviews the major findings on hypertension research and their implications and discusses evaluation of the patient with elevated blood pressure. "Why should we treat hypertension?" asks Dr Fröhlich. "Because it works—and most dramatically!"
The5ESSSwitching System: Applications Planning (1985)

The ESS™ system is designed for switching applications in rural, suburban, and metropolitan areas. It can function as a local, local/toll, or toll switch, and has features that make it suitable not only for use in the United States but in almost all countries. The modular design of the switch makes it particularly useful for solving wire center and network problems. This article discusses methods for solving such problems and presents some economic study results demonstrating the savings that can be achieved.
Allelic exclusion in transgenic mice carrying mutant human IgM genes. (1988)

Expression of the membrane-bound version of the human mu chain in transgenic mice results in the allelic exclusion of endogenous mouse Ig heavy chain genes (6). The secreted version of the human Ig transgene has no such effect. F1 hybrid animals that carry transgenes for both secreted and membrane-bound human mu chains produce both forms of the human heavy chain while strongly suppressing endogenous mouse mu expression. The simultaneous expression of the two rearranged transgenes in primary B cells suggests that allelic exclusion operates before the formation of a second functionally rearranged heavy chain gene in vivo.
Facile fabrication of large area nanostructures for efficient surface-enhanced Raman scattering (2006)

Large area SERS (surface-enhanced Raman scattering)-active films with closely packed nanoembossed Ag arrays were reproducibly fabricated by the replication method of polymer surfaces with nano-size grooved Al masters. Three different sizes (60, 105 and 420 nm) of nanoembossed polymer surface were produced from three different replication masters obtained by controlled anodization conditions of Al, which could be further coated with silver in various thicknesses by an ion sputtering technique. Nanoembossed Ag films with an emboss size of 420 nm, uniformly formed over all the areas of 1 × 1 cm2, exhibit very even SERS activity and the enhancement factor estimated using benzenethiol as a prototype adsorbate reaches as large as 6.6 × 105. Many replicas of polyethylene and polystyrene could be produced from one replication master by this simple replication method with high reproducibility. Almost the same SERS intensities were observed in ten different spots of each replica and twenty different replicas from one replication master.
Phloem sap proteins from Cucurbita maxima and Ricinus communis have the capacity to traffic cell to cell through plasmodesmata (1997)

In angiosperms, the functional enucleate sieve tube system of the phloem appears to be maintained by the surrounding companion cells. In this study, we tested the hypothesis that polypeptides present within the phloem sap traffic cell to cell from the companion cells, where they are synthesized, into the sieve tube via plasmodesmata. Coinjection of fluorescently labeled dextrans along with size-fractionated Cucurbita maxima phloem proteins, ranging in size from 10 to 200 kDa, as well as injection of individual fluorescently labeled phloem proteins, provided unambiguous evidence that these proteins have the capacity to interact with mesophyll plasmodesmata in cucurbit cotyledons to induce an increase in size exclusion limit and traffic cell to cell. Plasmodesmal size exclusion limit increased to greater than 20 kDa, but less than 40 kDa, irrespective of the size of the injected protein, indicating that partial protein unfolding may be a requirement for transport. A threshold concentration in the 20-100 nM range was required for cell-to-cell transport indicating that phloem proteins have a high affinity for the mesophyll plasmodesmal binding site(s). Parallel experiments with glutaredoxin and cystatin, phloem sap proteins from Ricinus communis, established that these proteins can also traffic through cucurbit mesophyll plasmodesmata. These results are discussed in terms of the requirements for regulated protein trafficking between companion cells and the sieve tube system. As the threshold value for plasmodesmal transport of phloem sap proteins falls within the same range as many plant hormones, the possibility is discussed that some of these proteins may act as long-distance signaling molecules.
Fabrication and characterization of a porous silicon based microarray for label-free optical monitoring of biomolecular interactions (2010)

We have fabricated a microarray of porous silicon Bragg reflectors on a crystalline silicon substrate using a technological process based on standard photolithography and electrochemical anodization of the silicon. The array density is of 170 elements/cm2 and each element has a diameter of 200 μm. The porous silicon structures have been used as platform to immobilize an amino terminated DNA single strand probe. All fabrication steps have been monitored by spectroscopic reflectometry, optical and electron microscopy, and Fourier transform infrared spectroscopy. A label-free detection method has been employed to investigate the hybridization between micromolar DNA probe and its complementary target. Due to fast and low cost production, good reproducibility, and high quality optical features, this platform could be adopted also for other different microarray applications such as proteomics and medical diagnostics.
Targeted Integration by Adeno-Associated Virus (2003)

The integration of foreign DNA into the genomes of host cells is of fundamental importance for viral oncology, evolution, transgenic organisms, and gene therapy applications. Expression of foreign genes in eukaryotic cells is highly dependent upon the efficiency of integration events and the site of insertion. Integration can sometimes have detrimental effects on the host cell, such as insertional mutagenesis or activation of proto-oncogenes. For gene therapy, it would therefore be attractive to target insertion to innocuous chromosomal sites. Understanding the mechanisms for integration of foreign DNA and target site selection is crucial for approaches where long-term expression from delivered transgenes is required.
Optical waveguide amplifier in Nd-doped glass writtenwith near-IR femtosecond laser pulses (2000)

A near-IR (775 nm) femtosecond laser has been used to directly write a 1 cm long optical waveguide in Nd-doped silicate glass. A gain of 1.5 dB/cm was obtained at a signal wavelength of 1054 nm for ~346 mW of 514 nm pump power, in front of the input coupling objective.
Paroxysmal Cold Haemoglobinuria (1984)

Paroxysmal cold haemoglobinuria (PCH) is a disease which today is met mainly in its acute form in children. The diagnosis is revealed by a careful serological examination. Case reports of four children with PCH are given in this paper. They all showed typical clinical pictures of PCH, and displayed the expected serological findings, including a bithermic autoantibody (haemolysin), the Donath-Landsteiner antibody. Children with PCH often require immediate transfusion therapy, but certain precautions should be taken regarding transfusion policy in these patients. When the acute phase is overcome, the prognosis is excellent.
Phase and Interface Engineering of Platinum–Nickel Nanowires for Efficient Electrochemical Hydrogen Evolution (2016)

The design of high-performance electrocatalysts for the alkaline hydrogen evolution reaction (HER) is highly desirable for the development of alkaline water electrolysis. Phase- and interface-engineered platinum-nickel nanowires (Pt-Ni NWs) are highly efficient electrocatalysts for alkaline HER. The phase and interface engineering is achieved by simply annealing the pristine Pt-Ni NWs under a controlled atmosphere. Impressively, the newly generated nanomaterials exhibit superior activity for the alkaline HER, outperforming the pristine Pt-Ni NWs and commercial Pt/C, and also represent the best alkaline HER catalysts to date. The enhanced HER activities are attributed to the superior phase and interface structures in the engineered Pt-Ni NWs.
The Click Reaction as an Efficient Tool for the Construction of Macrocyclic Structures (2013)

The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC, known as the click reaction) is an established tool used for the construction of complex molecular architectures. Given its efficiency it has been widely applied for bioconjugation, polymer and dendrimer synthesis. More recently, this reaction has been utilized for the efficient formation of rigid or shape-persistent, preorganized macrocyclic species. This strategy also allows the installment of useful functionalities, in the form of polar and function-rich 1,2,3-triazole moieties, directly embedded in the macrocyclic structures. This review analyzes the state of the art in this context, and provides some elements of perspective for future applications.