gebhart/patrepeval huggingface dataset:
Inhibition of lung cancer cell growth and induction of apoptosis after reexpression of 3p21.3 candidate tumor suppressor gene <i>SEMA3B</i> (2001)

Semaphorins SEMA3B and its homologue SEMA3F are 3p21.3 candidate tumor suppressor genes (TSGs), the expression of which is frequently lost in lung cancers. To test the TSG candidacy of SEMA3B and SEMA3F, we transfected them into lung cancer NCI-H1299 cells, which do not express either gene. Colony formation of H1299 cells was reduced 90% after transfection with wild-type SEMA3B compared with the control vector. By contrast, only 30-40% reduction in colony formation was seen after the transfection of SEMA3F or SEMA3B variants carrying lung cancer-associated single amino acid missense mutations. H1299 cells transfected with wild-type but not mutant SEMA3B underwent apoptosis. We found that lung cancers (n = 34) always express the neuropilin-1 receptor for secreted semaphorins, whereas 82% expressed the neuropilin-2 receptor. Because SEMA3B and SEMA3F are secreted proteins, we tested conditioned medium from COS-7 cells transfected with SEMA3B and SEMA3F and found that medium from wild-type SEMA3B transfectants reduced the growth of several lung cancer lines 30-90%, whereas SEMA3B mutants or SEMA3F had little effect in the same assay. Sequencing of sodium bisulfite-treated DNA showed dense methylation of CpG sites in the SEMA3B 5' region of lung cancers not expressing SEMA3B but no methylation in SEMA3B-expressing tumors. These results are consistent with SEMA3B functioning as a TSG, the expression of which is inactivated frequently in lung cancers by allele loss and promoter region methylation.
Foliar application of lipo-chitooligosaccharides (Nod factors) to tomato (<i>Lycopersicon esculentum</i>) enhances flowering and fruit production (2007)

Lipochitooligosaccharides (LCO) or Nod factors, which are rhizobia-produced signal molecules, induce deformation of legume root hairs. In addition to triggering legume plant nodulation, Nod factors influence cell division and promote somatic embryo generation in non-legume plants. This suggested to us the potential of using LCO to stimulate the development of tomato flowers and fruit. This study indicated that the foliar application o f LCO to tomato plants during the appropriate stages increased flower numbers and early fruiting in greenhouse trials. Flower stimulation by LCO occurred 1-2 wk after application and fruit numbers increased 2-4 wk after application. The accelerated flowering and fruiting resulted in an increase in tomato fruit yield. The most effective concentration of LCO was 50 ng per plant applied twice in the greenhouse, initially during the early flowering stage and again in the late flowering stage. A field trial in 2002 indicated that the optimal LCO application concentration was 10 ng per plant applied at the early flowering stage, which increased fruit yield and number by up to 29.8 and 29.4%, respectively. When plants received a second LCO application at the early fruiting stage, the fruit yield increased, but most were unmarketable green fruits. Analyses of yield data showed that the yield increase in field-grown tomatoes was due to an increase in the fruit number per plant, but not to individual fruit weight or fruit size. The average weight per fruit due to the treatment was not different from the control. A second field trial, carried out in 2003, showed that a foliar application of LCO at 50 ng per plant produced the best tomato yield. Our studies indicate that an LCO foliar application to tomatoes in the range of 10-50 ng per plant can increase early flowering and fruiting, which results in improved fruit yield. Key words: early flowering, foliar application, fruiting, growth promotion, lipo-chitooligosccharides, tomato yield
Rapid Prediction of Gross Energy and Utilizable Energy in Cereal Food Products Using Near-Infrared Reflectance Spectroscopy (2002)

Near-infrared (NIR) spectroscopy has been used in foods for the rapid assessment of several macronutrients; however, little is known about its potential for the evaluation of the utilizable energy of foods. Using NIR reflectance spectra (1104-2494 nm) of ground cereal products (n = 127) and values for energy measured by bomb calorimetry, chemometric models were developed for the prediction of gross energy and available energy of diverse cereal food products. Standard errors of cross-validation for NIR prediction of gross energy (range = 4.05-5.49 kcal/g), energy of samples after adjustment for unutilized protein (range = 3.99-5.38 kcal/g), and energy of samples after adjustment for unutilized protein and insoluble dietary fiber (range = 2.42-5.35 kcal/g) were 0.053, 0.053, and 0.088 kcal/g, respectively, with multiple coefficients of determination of 0.96. Use of the models on independent validation samples (n = 58) gave energy values within the accuracy required for U.S. nutrition labeling legislation. NIR spectroscopy, thus, provides a rapid and accurate method for predicting the energy of diverse cereal foods.
Water‐Based Synthesis of Zeolitic Imidazolate Framework‐90 (ZIF‐90) with a Controllable Particle Size (2013)

The ZIF code: ZIF-90 materials were successfully synthesized in an optimized water-based system. The particle size, ranging from micro- to nanoscales, could be controlled by different amounts of polyvinylpyrrolidone (PVP), Zn/imidazole-2-carboxaldehyde ratio and alcohol.
Real-time phase resolved optical coherence tomography and optical Doppler tomography using optical Hilbert Transformation (2002)

We have developed a novel real-time phase-resolved optical coherence tomography (OCT) and optical Doppler tomography (ODT) system using optical Hilbert transformation.By combining circularly polarized reference and linearly polarized sample signals, in-phase and quadrature interference components are produced in separate channels and treated as the real and imaginary parts of a complex signal to obtain the phase information directly.Using a resonant scanner at an axial scanning speed of 4 kHz in the reference arm of the interferometer, both structure and blood flow velocity images with 200 axial scans can be acquired at 20 frames per second with high sensitivity and large dynamic range.Real-time videos of in vivo blood flow in the chick chorioallantoic membrane using this interferometer are presented.
Diffuser augmentation of wind turbines (1976)

Wind tunnel investigation of models of two diffuser design concepts is directed toward unconventional, very short, cost-effective configurations. One approach uses the energetic external wind to prevent separation of the diffuser's internal boundary layer. Another method used high lift airfoil contours for the diffuser wall shape. Diffuser model tests have indicated almost a doubling of wind power extraction capability for DAWTs compared to conventional turbines. Economic studies of DAWTs have used these test data and recent (1975) cost projections of wind turbines with diameter. The specific power costs ($/kW) for a realistic DAWT configuration are found to be lower than conventional wind turbines for very large size rotors, above 50 meters diameter, and for rotor diameters less than about 20 meters. The cost-to-benefit assessment for intermediate size rotors is affected by the uncertainty band of cost for these rotor sizes.
Nd–Fe–B Permanent Magnet Materials (1987)

A comprehensive review of the Nd–Fe–B permanent magnet material is given. A historical survey, the basic magnetic properties of Nd2Fe14B and isomorphous compounds, a phase diagram for the ternary Nd–Fe–B system, processing techniques and magnetic properties of sintered Nd–Fe–B magnets, and the future directions for improvements of this type of permanent magnet are discussed.
Oxidized Phospholipids on apoB-100-Containing Lipoproteins: a Biomarker Predicting Cardiovascular Disease and Cardiovascular Events (2011)

Oxidative stress is a well-known etiologic factor in the development of cardiovascular disease. Oxidation of lipoproteins, and in particular of low density lipoprotein, is a necessary if not obligatory mechanism for the generation of macrophage-derived foam cells, the first major initiating factor in the development of an atherosclerotic plaque. Oxidation of lipoproteins does not result in the generation of a single, defined molecular species, but of a variety of oxidation-specific epitopes, such as oxidized phospholipids and malondialdehyde-lysine epitopes. Unique monoclonal antibodies have been developed to bind these well-defined epitopes, and have been used in in vitro assays to detect them on circulating lipoproteins present in plasma. This article will summarize the accumulating clinical data of one oxidation-specific biomarker, oxidized phospholipids (OxPL) on apoB-100 lipoproteins. Elevated levels of OxPL/apoB predict the presence and progression of coronary, femoral and carotid artery disease, are increased following acute coronary syndromes and percutaneous coronary intervention, and predict the development of death, myocardial infarction, stroke and need for revascularization in unselected populations. OxPL/apoB levels are independent of traditional risk factors and the metabolic syndrome, and enhance the risk prediction of the Framingham Risk Score. The OxPLs measured in this assay reflect the biological activity of the most atherogenic lipoprotein(a) (Lp(a)) particles, reflected in patients with high plasma Lp(a) levels with small apo(a) isoforms. The predictive value of OxPL/apoB is amplified by Lp(a) and phospholipases such as lipoprotein-associated phospholipase A(2) and secretory phospholipase A(2), which are targets of therapy in clinical trials. This assay has now been validated in over 10,000 patients and efforts are underway to make it available to the research and clinical communities.
Transform-based Arabic sign language recognition (2017)

Sign language is an independent language that uses gestures and body language to convey meaning. Sign language recognition facilities the communication between deaf and community. In this paper, we investigated the use of different transformation techniques for extraction and description of features from an accumulation of signs’ frames into a single image. We show the performance of three transformation techniques (viz. Fourier, Hartley, and Log-Gabor transforms) applied on the whole and slices of the accumulated sign’s image. In addition, different classification schemes are tested and compared. Overall system’s accuracy reached over 99% for Hartley transform which is comparable with other works using the same dataset.
Detection of <i>Escherichia coli</i> using immunomagnetic separation and bacteriophage amplification coupled with matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (2002)

The application of whole cell analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has emerged as a valuable tool for rapidly identifying/detecting bacteria. This technique requires minimal sample preparation and is simple to perform, but is generally limited to purified samples of bacteria at concentrations greater than 1.0 x 10(6) cells/mL. In this paper, we describe a bacterial detection method that integrates immunomagnetic separation with bacteriophage amplification prior to MALDI-MS analysis. The developed method consists of three main stages: (1) isolation of a target bacterium by immunomagnetic separation; (2) infection of the immuno-captured bacterium with a lytic bacteriophage; and (3) assay of infected medium for bacteriophage progeny using MALDI-MS to produce a molecular weight signal for the virus capsid protein. With this technique, the presence of Escherichia coli in broth was determined in less then 2 h total analysis time at a concentration of approximately 5.0 x 10(4) cells/mL.
Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5S RNA gene complex. (1992)

A series of polypeptides containing increasing numbers of zinc fingers of Xenopus transcription factor IIIA has been generated and binding to the 5S RNA gene internal control region has been studied in order to elucidate the mode of interaction of the individual fingers with DNA. By using a combination of DNase I footprinting, methylation interference, and differential binding to mixtures of DNA fragments differing in length by single base pairs, the binding sites for individual fingers have been defined. These results have led to a model for the interaction of transcription factor IIIA with the internal control region in which fingers 1-3 bind in the major groove of the promoter C block, fingers 7-9 bind in the major groove of the A block, and finger 5 binds in the major groove of the intermediate element. Fingers 4 and 6 each bind across the minor groove, spanning these promoter elements.
Bioconversion of curcumin into calebin-A by the endophytic fungus Ovatospora brasiliensis EPE-10 MTCC 25236 associated with Curcuma caesia (2019)

Calebin-A is a curcuminoid compound reported to be present in Curcuma longa rhizome. The current study was aimed to isolate and characterize calebin-A from Curcuma caesia rhizome and its production through biotransformation approach using endophytic fungus. C. caesia rhizomes of different ages were subjected to analysis in order to investigate the age at which maximum calebin-A content is present. HP-TLC profiles, HPLC retention times and mass spectrometry detector confirmed the occurrence of calebin-A in C. caesia rhizomes of 12 to 14 months of age but not in rhizomes younger to 12 months. Furthermore, an endophytic fungus strain, EPE-10 that was isolated from the medicinal plant C. caesia was identified as Ovatospora brasiliensis based on morphological and molecular characteristics. This strain O. brasiliensis was deposited to the culture collected centre, MTCC Chandigarh, India under the Budapest treaty and was designated with the Accession Number MTCC 25236. Biotransformation process was carried out at 37 ± 0.5 °C with shaking for 7 days after addition of 0.01% w/v curcumin. Extraction of biotransformed products was done by following partition method and the extracts obtained were analyzed using HPTLC, HPLC and LCMS. The data of the study suggested that O. brasiliensis MTCC 25236 was found to convert curcumin to calebin-A in a time dependant manner with optimum conversion at 48 h. Furthermore, O. brasiliensis MTCC 25236 was found to be positive for the Baeyer-Villiger monooxygenase (BVMOs) enzyme activity which could possibly be the mechanism of this bioconversion. The results of this study for the first time indicated that the endophytic fungus identified as O. brasiliensis MTCC 25236 isolated from the C. caesia rhizome could be a possible source for naturally producing calebin-A.
A Joint Many-Task Model: Growing a Neural Network for Multiple NLP Tasks (2016)

Transfer and multi-task learning have traditionally focused on either a single source-target pair or very few, similar tasks. Ideally, the linguistic levels of morphology, syntax and semantics would benefit each other by being trained in a single model. We introduce a joint many-task model together with a strategy for successively growing its depth to solve increasingly complex tasks. Higher layers include shortcut connections to lower-level task predictions to reflect linguistic hierarchies. We use a simple regularization term to allow for optimizing all model weights to improve one task's loss without exhibiting catastrophic interference of the other tasks. Our single end-to-end model obtains state-of-the-art or competitive results on five different tasks from tagging, parsing, relatedness, and entailment tasks.
Channel allocation for dynamic spectrum access cognitive networks using Localized island Genetic Algorithm (2009)

In our demonstration, we show how cognitive radios can be organized to form a cooperative ad-hoc cognitive radio network that utilizes the available spectrum opportunistically and efficiently through channel allocation while at the same time avoiding causing interference to primary users as they become active. Our cognitive radios are Software Defined Radios consisting of a Linux laptop and a Universal Software Radio Peripheral integrated with our extended implementation of the GNU Radio software package and our Localized island Genetic Algorithm implementation for the channel allocation.
Snf1 Is a Regulator of Lipid Accumulation in Yarrowia lipolytica (2013)

In the oleaginous yeast Yarrowia lipolytica, de novo lipid synthesis and accumulation are induced under conditions of nitrogen limitation (or a high carbon-to-nitrogen ratio). The regulatory pathway responsible for this induction has not been identified. Here we report that the SNF1 pathway plays a key role in the transition from the growth phase to the oleaginous phase in Y. lipolytica. Strains with a Y. lipolytica snf1 (Ylsnf1) deletion accumulated fatty acids constitutively at levels up to 2.6-fold higher than those of the wild type. When introduced into a Y. lipolytica strain engineered to produce omega-3 eicosapentaenoic acid (EPA), Ylsnf1 deletion led to a 52% increase in EPA titers (7.6% of dry cell weight) over the control. Other components of the Y. lipolytica SNF1 pathway were also identified, and their function in limiting fatty acid accumulation is suggested by gene deletion analyses. Deletion of the gene encoding YlSnf4, YlGal83, or YlSak1 significantly increased lipid accumulation in both growth and oleaginous phases compared to the wild type. Furthermore, microarray and quantitative reverse transcription-PCR (qRT-PCR) analyses of the Ylsnf1 mutant identified significantly differentially expressed genes during de novo lipid synthesis and accumulation in Y. lipolytica. Gene ontology analysis found that these genes were highly enriched with genes involved in lipid metabolism. This work presents a new role for Snf1/AMP-activated protein kinase (AMPK) pathways in lipid accumulation in this oleaginous yeast.
Use of the surface proteins GapC and Mig of<i>Streptococcus dysgalactiae</i>as potential protective antigens against bovine mastitis (2004)

Streptococcus dysgalactiae is a significant pathogen associated with bovine mastitis in lactating and nonlactating dairy cows, causing a severe inflammatory response of the mammary gland, which results in major economic losses to the dairy industry. Two proteins from S. dysgalactiae strain SDG8 were tested for their protective capacity against a homologous bacterial challenge in a dry cow model. The first was a bovine plasmin receptor protein (GapC), which shares 99.4% sequence identity to the plasmin-binding Plr protein of group A streptococci. The second protein product was Mig, a alpha2-M-, IgG-, and IgA-binding protein present on the cell surface of SDG8. We investigated the efficacy of immunization with purified recombinant forms of GapC and Mig by measuring the number of somatic cells and assessing the presence of the challenge strain in mammary secretions following challenge. In this model, we found that, although the number of quarters containing SDG8 was significantly reduced in the GapC- but not in the Mig-immunized animals, the somatic cell counts from teat secretions were significantly decreased in both the GapC and Mig vaccinates.
Laboratory Evaluation of Stainless Steel Filters for Control of Particulate Emissions (2011)

This research developed a method to control particulate emissions from Army demilitarization furnaces by developing high temperature filters capable of capturing particulate emissions, including the heavy metal PM2.5.Custom manufactured stainless steel filters were evaluated in a filter test setup based on American Society of Heating, Refrigerating, and Air-Conditioning Engineers (ASHRAE) and American Society for Testing and Materials (ASTM) standard protocols used to characterize flat panel filters.Experimental studies using an in-house testing system on pressure drop versus flow rate, particle penetration, and dust holding capacity were performed for each filter.Experimental results showed that, as the quantity of dust increases, pressure drop increases linearly.In the presence of dust, a cake layer forms reducing effective pore size and therefore increasing the filter efficiency.Preliminary results showed that these filters offer a reusable, easily cleanable, cost-effective, and compact particulate filtration system for the Army mobile and stationary combustion systems.Future research is recommended to determine compatibility of the filter material to the operating temperature, pressure, air superficial velocity, and other physicochemical conditions, and whether modifying the filter system by coating with adsorbent material and tack polymers may enhance the separation of metals and other fine particulates.
Design and use of the biomolecular interaction network database (bind) for storing and analyzing protein-protein interaction data (2003)

As genomics and proteomics technologies such as mass spectrometry, yeast two-hybrid, phage display and genetic interaction screens become more sensitive and robust, they are becoming more automated and high-throughput. These experimental systems are currently providing a wealth of data on genetic and molecular interactions and post-translational protein modifications. The Biomolecular Interaction Network Database (BIND - http://bind.ca) has been designed to store details about these molecular and genetic interactions, complexes and pathways and thus captures proteomics data in a computer readable format. Chemical reactions, photochemical activation and conformational changes can be described down to the atomic level of detail. Everything from small graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for full pathway kinetic simulations. Currently, BIND is a web-based system that allows the database to be queried and for records to be entered. A Java applet to visually navigate the database and a BLAST against BIND service are both available via the web. BIND is an open community effort. All BIND records are in the public domain and source code for the project is made freely available under the GNU Public License. The system is designed so that both users and a curation staff can submit interactions described in the literature, which are then vetted. BIND has been used to manage and automatically discover new knowledge residing in large yeast protein-protein and genetic interaction networks in Saccharomyces cerevisiae determined using mass-spectrometry, phase-display, yeast two-hybrid and roboticized synthetic lethal screens. A system, called MCODE (Molecular Complex Detection), for automatically recognizing molecular complexes in large molecular interaction networks, has been devised. MCODE is based on the notion that densely connected regions of a molecular network, or graph, represent molecular complexes. The BIND project illustrates how a structured software development process focusing on the design phase provides a sturdy foundation for the future implementation of bioinformatics tools that solve real biological problems.
Low Complexity Fixed-Point Approximation of Inverse Discrete Cosine Transform (2007)

This paper presents an efficient algorithm for computing the Inverse discrete cosine transform (IDCT) for image and video coding applications. This algorithm was submitted in response to MPEG's call for proposals for ISO/IEC 23002-2 (fixed-point 8times8 IDCT and DCT) standard, and was subsequently adopted in the Working Draft 1 of this standard. Our proposed algorithm is a multiplication-free implementation. It is based on a modification of Arai, Agui, and Nakajima's (AAN) factorization, and requires only 42 addition and 16 shift operations per scaled ID transform. Each register in our scaled ID transform requires at most 22 bits. This implementation complies with the MPEG IDCT precision specification ISO/IEC 23002-1.