gebhart/patrepeval huggingface dataset:
Recognition of Anionic Porphyrins by DNA Aptamers (1996)

DNA sequences were isolated by in vitro selection for binding to N-methylmesoporphyrin IX (NMM), a molecule that behaves as a stable transition-state analogue for porphyrin chelatases. Clones approximately 280 and approximately 120 nucleotides long were obtained, which bound to NMM with sub-micromolar affinity but bound mesoporphyrin IX (MPIX), as well as various metalloderivatives of MPIX, with lower affinity. Footprinting experiments with dimethyl sulfate, DNase I, and bound hemin molecules activated by superoxide identified a series of short guanine-rich motifs to be the binding sites for the various porphyrins. One clone, PS2, examined in depth, gave a methylation footprint with bound NMM but not with bound MPIX nor with a number of metalloporphyrins. The binding domain PS2, synthesized as a short oligonucleotide, itself showed high-affinity binding to NMM. The binding sequences from different clones were loosely homologous, and the footprinting data were consistent with their folding to form one or more guanine quartets in the presence of NMM. Ultraviolet--visible absorption and circular dichroism spectroscopy of the DNA--NMM complexes indicates, however, that the interaction is not primarily intercalative in nature. The preferential binding of NMM by these aptamers raises the possibility of their being able to catalyze the chelation of metal ions by the porphyrin MPIX.
Inhibition of cancer cell proliferation and prostaglandin E2 synthesis by Scutellaria baicalensis. (2003)

Scutellaria baicalensis is a widely used Chinese herbal medicine that has been used historically in anti-inflammatory and anticancer therapy. The purpose of this study is to verify its anticancer activity on head and neck squamous cell carcinoma (HNSCC) in vitro and in vivo and to investigate its effect on cyclooxygenase-2 (COX-2), which converts arachidonic acid to prostaglandin E(2) (PGE(2)) and is highly expressed in HNSCC. Two human HNSCC cell lines (SCC-25 and KB) and a nontumorigenic cell line (HaCaT) were tested in vitro for growth inhibition, proliferation cell nuclear antigen expression, and COX-2 activity and expression after treatment with Scutellaria baicalensis extract. Its effects were compared with those of baicalein (a flavonoid isolated from Scutellaria baicalensis), indomethacin (a nonselective COX inhibitor), and celecoxib (a selective COX-2 inhibitor). Four nude mice with s.c. inoculation of KB cells were tested for its anticancer activity in vivo by oral administration of Scutellaria baicalensis at a dose of 1.5 mg/mouse (75 mg/kg), five times/week for 7 weeks. Scutellaria baicalensis and other agents demonstrated a strong growth inhibition in both tested human HNSCC cell lines. No growth inhibition of HaCaT cells was observed with Scutellaria baicalensis. The IC(50)s were 150 micro g/ml for Scutellaria baicalensis, 25 micro M for celecoxib, and 75 micro M for baicalein and indomethacin. Scutellaria baicalensis, as well as celecoxib and indomethacin, but not baicalein, suppressed proliferation cell nuclear antigen expression and PGE(2) synthesis in both cell types. Scutellaria baicalensis inhibited COX-2 expression, whereas celecoxib inhibited COX-2 activity directly. A 66% reduction in tumor mass was observed in the nude mice. Scutellaria baicalensis selectively and effectively inhibits cancer cell growth in vitro and in vivo and can be an effective chemotherapeutic agent for HNSCC. Inhibition of PGE(2) synthesis via suppression of COX-2 expression may be responsible for its anticancer activity. Differences in biological effects of Scutellaria baicalensis compared with baicalein suggest the synergistic effects among components in Scutellaria baicalensis.
A fully synthetic self-adjuvanting globo H-Based vaccine elicited strong T cell-mediated antitumor immunity (2015)

Therapeutic cancer vaccines based on the abnormal glycans expressed on cancer cells, such as the globo H antigen, have witnessed great progress in recent years. For example, the keyhole limpet hemocyanin (KLH) conjugate of globo H has been on clinical trials as a cancer vaccine. However, such vaccines have intrinsic problems, such as inconsistence in eliciting T cell-mediated immunity in cancer patients and difficult quality control. To address the issue, a structurally defined fully synthetic glycoconjugate vaccine composed of globo H and monophosphoryl lipid A (MPLA) was developed. The new vaccine was shown to elicit robust IgG1 antibody responses and T cell-dependent immunity, which is desired for anticancer vaccine, and induce significantly faster and stronger immune responses than the globo H-KLH conjugate. Moreover, it was self-adjuvanting, namely, inducing immune responses without the use of an external adjuvant, thus MPLA was not only a vaccine carrier but also a build-in adjuvant. It was also found that antibodies induced by the new vaccine could selectively bind to and mediate strong complement-dependent cytotoxicity to globo H-expressing MCF-7 cancer cell. All of the results have demonstrated that the globo H-MPLA conjugate is a better cancer vaccine than the globo H-KLH conjugate under experimental conditions and is worth further investigation and development.
A phrase-based unigram model for statistical machine translation (2003)

In this paper, we describe a phrase-based unigram model for statistical machine translation that uses a much simpler set of model parameters than similar phrase-based models. The units of translation are blocks - pairs of phrases. During decoding, we use a block unigram model and a word-based trigram language model. During training, the blocks are learned from source interval projections using an underlying word alignment. We show experimental results on block selection criteria based on unigram counts and phrase length.
How I Came to Work at Wendy's (2010)

A series of drawn images documenting a man's journey from unemployed to employed at Wendy's
Demonstration of megavoltage and diagnostic x‐ray imaging with hydrogenated amorphous silicon arrays (1992)

Flat-panel imagers consisting of the first large area, self-scanning, pixelated, solid-state arrays made with hydrogenated amorphous silicon (a-Si:H) are under development by the authors for applications in diagnostic x-ray and megavoltage radiotherapy imaging. The arrays, designated by the acronym MASDA for multi-element amorphous silicon detector array, consist of a two-dimensional array of a-Si:H photodiodes and thin-film transistors and are used in conjunction with scintillating materials. Imagers utilizing MASDA arrays offer a variety of advantages over existing technologies. This article presents initial megavoltage and diagnostic-quality x-ray images taken with several such arrays including the first examples of anatomical-phantom images. The external readout electronics and imaging techniques required to obtain such images are outlined, the construction, operation, and advantages of the arrays briefly reviewed, and the future potential of this new technology discussed.
Lactobacillus hilgardii plasmid pLAB1000 consists of two functional cassettes commonly found in other gram-positive organisms (1990)

A Lactobacillus hilgardii plasmid, pLAB1000, was studied to understand the organization of autonomous replicons from lactobacilli. Two cassettes could be identified. First, the replication region consisted of a sequence coding for a replication protein (Rep) and its corresponding target site, similar to those from plasmids pUB110, pC194 (Staphylococcus aureus), pFTB14, pBAA1 (Bacillus sp.), and pLP1 (Lactobacillus sp.). Sequence analysis indicated the possible synthesis of an antisense RNA that might regulate Rep production. The results also suggested that pLAB1000 replicates via a single-stranded DNA intermediate, and a putative lagging-strand initiation site was found that had similarities to those of alpha 3, St-1, and G4 isometric bacteriophages. The second cassette of pLAB1000 consisted of a sequence coding for a putative mobilization protein (Mob) and its corresponding RSA site. This cassette was similar to those found in pT181, pUB110, pE194 (S. aureus), and pG12 (Bacillus sp.), and it was found to be conserved among different Lactobacillus plasmid replicons. The origin and evolution of these functional cassettes are also discussed.
Microfabrication technologies in dielectrophoresis applications—A review (2012)

DEP is an established technique for particle manipulation. Although first demonstrated in the 1950s, it was not until the development of miniaturization techniques in the 1990s that DEP became a popular research field. The 1990s saw an explosion of DEP publications using microfabricated metal electrode arrays to sort a wide variety of cells. The concurrent development of microfluidics enabled devices for flow management and better understanding of the interaction between hydrodynamic and electrokinetic forces. Starting in the 2000s, alternative techniques have arisen to overcome common problems in metal-electrode DEP, such as electrode fouling, and to increase the throughput of the system. Insulator-based DEP and light-induced DEP are the most significant examples. Most recently, new 3D techniques such as carbon-electrode DEP, contactless DEP, and the use of doped PDMS have further simplified the fabrication process. The constant desire of the community to develop practical solutions has led to devices which are more user friendly, less expensive, and are capable of higher throughput. The state-of-the-art of fabricating DEP devices is critically reviewed in this work. The focus is on how different fabrication techniques can boost the development of practical DEP devices to be used in different settings such as clinical cell sorting and infection diagnosis, industrial food safety, and enrichment of particle populations for drug development.
Bispecific digoxigenin-binding antibodies for targeted payload delivery (2011)

Bispecific antibodies that bind cell-surface targets as well as digoxigenin (Dig) were generated for targeted payload delivery. Targeting moieties are IgGs that bind the tumor antigens Her2, IGF1R, CD22, or LeY. A Dig-binding single-chain Fv was attached in disulfide-stabilized form to C termini of CH3 domains of targeting antibodies. Bispecific molecules were expressed in mammalian cells and purified in the same manner as unmodified IgGs. They are stable without aggregation propensity and retain binding specificity/affinity to cell-surface antigens and Dig. Digoxigeninylated payloads were generated that retain full functionality and can be complexed to bispecific antibodies in a defined 21 ratio. Payloads include small compounds (Dig-Cy5, Dig-Doxorubicin) and proteins (Dig-GFP). Complexed payloads are targeted by the bispecifics to cancer cells and because these complexes are stable in serum, they can be applied for targeted delivery. Because Dig bispecifics also effectively capture digoxigeninylated compounds under physiological conditions, separate administration of uncharged Dig bispecifics followed by application of Dig payload is sufficient to achieve antibody-mediated targeting in vitro and in vivo.
Adenosine A2A or A3 receptors are required for inhibition of inflammation by methotrexate and its analog MX‐68 (2003)

These findings confirm that adenosine, acting at A(2A) and A(3) receptors, is a potent regulator of inflammation. Moreover, these results provide strong evidence that adenosine, acting at either or both of these receptors, mediates the antiinflammatory effects of methotrexate and its analog MX-68.
Eclampsia in the United Kingdom (1994)

Eclampsia occurs in nearly one in 2000 maternities in the United Kingdom and is associated with high maternal morbidity and fatality in cases. It may present unheralded by warning signs. Preterm and antenatal eclampsia seem to be particularly severe.
Frequency of NOD2/CARD15 gene polymorphisms in the Algerian pediatric Crohn's disease patients. (2014)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
ES-like cell cultures derived from early zebrafish embryos. (1995)

Pluripotent embryonic stem (ES) cell cultures provide an efficient method for genome manipulation with many applications in marine biotechnology. To develop this technology we have been working to derive fish ES cell lines for in vitro studies of embryo cell growth and differentiation and for the generation of transgenic fish. Zebrafish embryonal cell cultures were derived from blastula-stage embryos in LDF medium supplemented with fetal bovine serum, trout serum, trout embryo extract, selenium, insulin, and leukemia inhibitory factor. Cultures derived under these conditions on feeder layers of zebrafish embryonic fibroblasts possessed a diploid karyotype and exhibited an ES-like morphology with elevated levels of alkaline phosphatase enzyme activity. Injection of primary cell cultures derived from embryos of transgenic fish carrying neo produced chimeric fish detected by polymerase chain reaction analysis. Embryo cells cultured on poly-D-lysine substrate in the presence of retinoic acid or Buffalo rat liver cell-conditioned medium (BRL-CM) and a reduced serum concentration differentiated into neuronal cell types exhibiting elevated levels of acetylcholinesterase enzyme activity and expression of neurofilament and glial fibrillary acidic protein.
Human monoclonal antibodies specific to hepatitis B virus generated in a human/mouse radiation chimera: the Trimera system (1998)

An approach to develop fully human monoclonal antibodies in a human/mouse radiation chimera, the Trimera system, is described. In this system, functional human lymphocytes are engrafted in normal strains of mice which are rendered immuno-incompetent by lethal total body irradiation followed by radioprotection with severe combined immunodeficient (SCID) mouse bone marrow. Following transplantation, human lymphocytes colonize murine lymphatic organs and secrete human immunoglobulins. We have established this system as a tool to develop fully human monoclonal antibodies, and applied it for the generation of monoclonal antibodies specific for hepatitis B virus surface antigen. A strong memory response to hepatitis B surface antigen was elicited in Trimera engrafted with lymphocytes from human donors positive for antibodies to hepatitis B surface antigen. The human specific antibody fraction in the Trimera was 10(2)-10(3)-fold higher as compared with that found in the donors. Spleens were harvested from Trimera mice showing high specific-antibody titres and cells were fused to a human-mouse heteromyeloma fusion partner. Several stable hybridoma clones were isolated and characterized. These hybridomas produce high-affinity, IgG, anti-hepatitis B surface antigen antibodies demonstrating the potential of the Trimera system for generating fully human monoclonal antibodies. The biological function and the neutralizing activity of these antibodies are currently being tested.
Regulation of human neutrophil Fcγ receptor IIa by C5a receptor promotes inflammatory arthritis in mice (2010)

Human and murine activating FcγR on neutrophils are not functionally equivalent, and in humans, they may play a primary role in arthritis. Crosstalk between neutrophil C5aR and FcγRIIa is essential for disease progression, thus highlighting a new aspect of complement during the effector phase of inflammatory arthritis.
Separation of cells labeled with immunospecific iron dextran microspheres using high gradient magnetic chromatography (1984)

Immunospecific magnetic microspheres, consisting of ferromagnetic iron dextran conjugated to Protein A, were used to specifically label red blood cells (RBC) for cell separation studies using high gradient magnetic chromatography ( HGMC ). When 10(7)-10(8) RBC labeled with Protein A-iron dextran microspheres were applied to a column containing 30 mg stainless steel wire placed in a 7.5 kilogauss magnetic field, 96 +/- 2% of the cells were retained in the column. These cells could be eluted by removing the magnetic field and mechanically agitating the column. The retention of labeled cells by HGMC was shown to be dependent on the applied magnetic field and the amount of wire packed into the column. HGMC in conjunction with cell labeling with immunospecific iron dextran microspheres have useful applications for the separation of specific cell types.
NMDA Receptor Antagonists for Treatment of Depression (2013)

Depression is a psychiatric disorder that affects millions of people worldwide. Individuals battling this disorder commonly experience high rates of relapse, persistent residual symptoms, functional impairment, and diminished well-being. Medications have important utility in stabilizing moods and daily functions of many individuals. However, only one third of patients had considerable improvement with a standard antidepressant after 2 months and all patients had to deal with numerous side effects. The N-methyl-d-aspartate (NMDA) receptor family has received special attention because of its critical role in psychiatric disorders. Direct targeting of the NMDA receptor could result in more rapid antidepressant effects. Antidepressant-like effects of NMDA receptor antagonists have been demonstrated in different animal models. MK-801 (a use-dependent channel blocker), and CGP 37849 (an NMDA receptor antagonist) have shown antidepressant properties in preclinical studies, either alone or combined with traditional antidepressants. A recent development is use of ketamine clinically for refractory depression. The purpose of this review is to examine and analyze current literature on the role of NMDA receptor antagonists for treatment of depression and whether this is a feasible route in drug discovery.
Site-directed Mutagenesis and Characterization of Uracil-DNA Glycosylase Inhibitor Protein (1997)

Bacteriophage PBS2 uracil-DNA glycosylase inhibitor (Ugi) protein inactivates uracil-DNA glycosylase (Ung) by acting as a DNA mimic to bind Ung in an irreversible complex. Seven mutant Ugi proteins (E20I, E27A, E28L, E30L, E31L, D61G, and E78V) were created to assess the role of various negatively charged residues in the binding mechanism. Each mutant Ugi protein was purified and characterized with respect to inhibitor activity and Ung binding properties relative to the wild type Ugi. Analysis of the Ugi protein solution structures by nuclear magnetic resonance indicated that the mutant Ugi proteins were folded into the same general conformation as wild type Ugi. All seven of the Ugi proteins were capable of forming a Ung.Ugi complex but varied considerably in their individual ability to inhibit Ung activity. Like the wild type Ugi, five of the mutants formed an irreversible complex with Ung; however, the binding of Ugi E20I and E28L to Ung was shown to be reversible. The tertiary structure of [13C,15N]Ugi in complex with Ung was determined by solution state multi-dimensional nuclear magnetic resonance and compared with the unbound Ugi structure. Structural and functional analysis of these proteins have elucidated the two-step mechanism involved in Ung.Ugi association and irreversible complex formation.
Multifunctional magnetic nanoparticles for medical imaging applications (2009)

Magnetic nanoparticles (MNPs) have attracted enormous research attention due to their unique magnetic properties that enable the detection by the non-invasive medical imaging modality-magnetic resonance imaging (MRI). By incorporating advanced features, such as specific targeting, multimodality, therapeutic delivery, the detectability and applicability of MNPs have been dramatically expanded. A delicate design on structure, composition and surface chemistry is essential to achieving desired properties in MNP systems, such as high imaging contrast and chemical stability, non-fouling surface, target specificity and/or multimodality. This article presents the design fundamentals on the development of MNP systems, from discussion of material selection for nanoparticle cores and coatings, strategies for chemical synthesis and surface modification and their merits and limitations, to conjugation of special biomolecules for intended functions, and reviews the recent advances in the field.
Multispectral interference filter arrays with compensation of angular dependence or extended spectral range (2015)

Thin film Fabry-Perot filter arrays with high selectivity can be realized with a single patterning step, generating a spatial modulation of the effective refractive index in the optical cavity. In this paper, we investigate the ability of this technology to address two applications in the field of image sensors. First, the spectral tuning may be used to compensate the blue-shift of the filters in oblique incidence, provided the filter array is located in an image plane of an optical system with higher field of view than aperture angle. The technique is analyzed for various types of filters and experimental evidence is shown with copper-dielectric infrared filters. Then, we propose a design of a multispectral filter array with an extended spectral range spanning the visible and near-infrared range, using a single set of materials and realizable on a single substrate.
Expanding the input expressivity of smartwatches with mechanical pan, twist, tilt and click (2014)

Smartwatches promise to bring enhanced convenience to common communication, creation and information retrieval tasks. Due to their prominent placement on the wrist, they must be small and otherwise unobtrusive, which limits the sophistication of interactions we can perform. This problem is particularly acute if the smartwatch relies on a touchscreen for input, as the display is small and our fingers are relatively large. In this work, we propose a complementary input approach: using the watch face as a multi-degree-of-freedom, mechanical interface. We developed a proof of concept smartwatch that supports continuous 2D panning and twist, as well as binary tilt and click. To illustrate the potential of our approach, we developed a series of example applications, many of which are cumbersome -- or even impossible -- on today's smartwatch devices.
Evaluation of Waste Activated Sludge (Citrus) as a Poultry Feed Ingredient (1976)

Cobb color-sexed broilers were fed diets containing either 0.0, 2.5, 5.0 or 10.0 percent citrus sludge. Three replications of ten males and ten females each were randomly selected from each treatment at the end of the eight-week feeding period. No significant (P< 0.05) differences among levels of citrus sludge were found in carcass weight, percent cooking loss, shear force or sensory evaluation. Eggs collected from Babcock B-300 hens fed diets prepared with citrus sludge at levels of 0.0, 2.5, 5.0, 7.5 and 20.0% were examined for differences in yolk color and development of off-flavors. Color differences (P < 0.05) were observed by reflectance colorimetery and the taste panel. The hue of the yolks increased (was more orange) as the dietary citrus sludge levels were increased. No significant flavor differences were detected by the taste panel for either the yolk or albumen.