gebhart/patrepeval huggingface dataset:
The<i>Xenopus Brachyury</i>promoter is activated by FGF and low concentrations ofactivinandsuppressed by high concentrationsof activin and by paired-type homeodomain proteins (1997)

The mesoderm of Xenopus laevis arises through an inductive interaction in which signals from the vegetal hemisphere of the embryo act on overlying equatorial cells. One candidate for an endogenous mesoderm-inducing factor is activin, a member of the TGFbeta superfamily. Activin is of particular interest because it induces different mesodermal cell types in a concentration-dependent manner, suggesting that it acts as a morphogen. These concentration-dependent effects are exemplified by the response of Xbra, expression of which is induced in ectodermal tissue by low concentrations of activin but not by high concentrations. Xbra therefore offers an excellent paradigm for studying the way in which a morphogen gradient is interpreted in vertebrate embryos. In this paper we examine the trancriptional regulation of Xbra2, a pseudoallele of Xbra that shows an identical response to activin. Our results indicate that 381 bp 5' of the Xbra2 transcription start site are sufficient to confer responsiveness both to FGF and, in a concentration-dependent manner, to activin. We present evidence that the suppression of Xbra expression at high concentrations of activin is mediated by paired-type homeobox genes such as goosecoid, Mix.1, and Xotx2.
Monoclonal antibodies specific for the carboxy terminus of simian virus 40 large T antigen (1984)

Three mouse hybridomas secreting antibodies against the undecapeptide Lys-Pro-Pro-Thr-Pro-Pro-Pro-Glu-Pro-Glu-Thr, corresponding to the carboxy terminus of simian virus 40 large T antigen, were isolated and cloned. A sensitive enzyme-linked immunosorbent assay was used to characterize the properties of the monoclonal antibodies. All three hybridomas, designated KT1, KT3, and KT4, produced antibodies that immunoprecipitated large T. The antibodies differed in their affinities for the peptide and for the native protein. Antibodies from KT3 precipitated large T better than those from KT1 or KT4. KT3 antibodies also had the highest affinity for the free peptide (5.2 X 10(6) M-1) as determined by radioimmunoassay; KT1 and KT4 antibodies had ca. 5- and 1,000-fold lower affinities, respectively. Inhibition studies with shorter peptides, overlapping the undecapeptide, revealed the approximate regions recognized by the different monoclonal antibodies. KT3 antibodies bound to a region within the carboxy-terminal six amino acids of large T. Antibodies from KT1 and KT4 reacted with sequences located further towards the amino terminus of the undecapeptide. Surprising results were obtained with KT4 antibodies. Their binding to the undecapeptide was completely inhibited by the undecapeptide itself or the carboxy-terminal hexapeptide. The carboxy-terminal pentamer, on the other hand, slightly enhanced binding, and the carboxy-terminal tetramer, Glu-Pro-Glu-Thr, was strongly stimulatory. A model for this effect is proposed. Using the enzyme-linked immunosorbent assay, we confirmed previous studies (W. Deppert and G. Walter, Virology 122:56-70, 1982) which found that antiserum against sodium dodecyl sulfate-denatured large T reacts strongly with the carboxy terminus of large T. By inhibition studies, we identified the approximate region within the undecapeptide recognized by anti-sodium dodecyl sulfate-denatured large T and compared this region with the region identified by antipeptide serum.
Survival of <i>Legionella pneumophila</i> within cysts of <i>Acanthamoeba polyphaga</i> following chlorine exposure (1990)

The association between Legionella pneumophila and the free‐living amoeba Acanthamoeba polyphaga was studied. Intracellular growth of L. pneumophila within amoebic trophozoite was confirmed by kinetic growth experiments, light and electron microscopy. Cysts produced from infected trophozoites were found to protect the legionellas from at least 50 mg/l free chlorine. The ability of L. pneumophila to survive within the cysts of A. polyphaga is suggested as a possible mechanism by which the organism evades disinfection and spreads to colonize new environments.
Hydraulic Conductivity Performance of Geosynthetic Clay Liner (GCL) Permeated with Inorganic Chemical Solutions (1999)

Hydraulic conductivity performance of a geosynthetic clay liner permeated with inorganic chemical solutions is discussed. Although GCLs are expected to be applied to bottom liners and/or covers to contain wastes in landfills, limited data on the chemical compatibility are available. In this study, the brief literature review as well as the hydraulic conductivity test results are presented. The literature review shows there are some significant factors affecting the hydraulic conductivity values on GCLs permeated with chemical solutions. For the experimental work, hydraulic conductivity tests were conducted on a needle-punched GCL with inorganic chemical solutions by using flexible-wall permeameters to assess the effect of the concentration, pH, and other factors. Experimental results showed (1) a significant increase in hydraulic conductivity occur between 0.01-0.1M in concentration for divalent and trivalent cations, (2) monovalent cations has less effect on hydraulic conductivity than divalent cations, (3) the hydraulic conductivity is affected by both pH and cation concentrations, and (4) an excellent agreement between the hydraulic conductivity and free swell volume is achieved.
Magnetic resonance imaging of the kidneys: current status. (1994)

Magnetic resonance imaging (MRI) differs fundamentally from other imaging techniques, since for the first time one method permits simultaneous assessment of macroscopic changes in the kidneys and evaluation of renal functional derangements. To provide morphological information that may compete with the results of computed tomography (CT) and ultrasonography (US), special techniques like artifact compensation, fast imaging, and fat suppression have to be employed. The additional use of a renally eliminated paramagnetic contrast agent permits assessment of parenchymal perfusion and visualization of the passage of the contrast medium, providing information about renal excretory function. Results and clinical utility of state of the art MRI can be summarized as follows: (a) MR is not a screening method; sensitivity is, however, similar to CT when fat suppression and contrast agents are used. (b) Classification of renal masses is almost restricted to the differentiation of cystic, fat-containing, and solid lesions. (c) Contrast-enhanced MRI helps to assess large retroperitoneal masses and to classify them as intra- or extrarenal. (d) Accurate staging of renal cancers is possible; thus, MRI is a good alternative when CT yields uncertain findings and for patients with known contraindications to the administration of iodinated contrast agents. (e) Contrast-enhanced dynamic MRI studies provide semiquantitative evaluation of global and segmental renal function. (f) MR angiography offers the possibility to evaluate renal arteries and veins.
Development of RGD peptides grafted onto silica surfaces: XPS characterization and human endothelial cell interactions (1999)

The attachment of human umbilical vein endothelial cells (HUVECs) on substrates that had been covalently grafted with the cell adhesion peptides Arg-Gly-Asp (RGD) was investigated. This approach was used to provide substrates that are adhesive to cells even in the absence of serum proteins and to cells that have had no prior treatment of the surface with proteins that promote cell adhesion. We wanted to improve control of cellular interactions with cell-adhesive materials by providing fixedly bound adhesion ligands. Silica was examined as a model surface. The peptides were grafted using three different steps: grafting of aminosilane molecules; reaction with a maleimide molecule; and immobilization of cell-binding peptides containing the RGD sequence. The RGD-grafted surface was characterized by X-ray photoelectron spectroscopy (XPS) and contact-angle measurements.
Strategies for development of vaccines for control of ixodid tick species (2006)

Ticks are distributed worldwide and impact human and animal health, as well as food animal production. Control of ticks has been primarily by application of acaricides, which has resulted in selection of resistant ticks and environmental pollution. Vaccines have been shown to be a feasible tick control method that offers a cost-effective, environmentally friendly alternative to chemical control. However, identification of tick-protective antigens remains the limiting step in vaccine development. Tick antigens exposed naturally to the host during tick feeding and those concealed have both shown promise as candidate vaccine antigens. Development of vaccines against multiple tick species may be possible using highly conserved tick-protective antigens or by antigens showing immune cross-reaction to different tick species. Vaccines made from a combination of key protective antigens may greatly enhance vaccine efficacy. Preliminary studies have suggested the possibility of vaccine strategies directed toward both tick control and the blocking of pathogen transmission. Characterization of the tick genomes will have a great impact on the discovery of new protective antigens. The future of research directed toward tick vaccine development is exciting because of new and emerging technologies for gene discovery, and vaccine formulation and delivery.
Review Application of RNA-seq to reveal the transcript profile in bacteria (2011)

The large number of microbial genomes deposited in databanks has opened the door for in-depth studies of organisms, including post-genomics investigations. Thanks to new generation sequencing technology, these studies have made advances that have lead to extraordinary discoveries in bacterial transcriptomics. In this review, we describe bacterial RNA sequencing studies that use these new techniques. We also examined the advantages and biases of these new generation technologies; advances in bioinformatics make it possible to overcome the biases, providing interesting and surprising results.
Realization of a narrowband single wavelength microring mirror (2011)

We present a small footprint narrowband on-chip mirror made by integration of a distributed Bragg reflector (DBR) inside a microring resonator. The DBR covers half of the ring’s circumference and is only reflective at one of the ring resonances. Design, fabrication, and characterization of the proposed device are presented. A single reflection peak with maximum power reflectivity of 92.3% and full width at half maximum of 0.4 nm is demonstrated. The device has potential application as an in-line mirror for low-threshold, narrow linewidth single mode laser diodes.
Crowdsourcing Natural Products Discovery to Access Uncharted Dimensions of Fungal Metabolite Diversity (2013)

A fundamental component for success in drug discovery is the ability to assemble and screen compounds that encompass a broad swath of biologically relevant chemical-diversity space. Achieving this goal in a natural-products-based setting requires access to a wide range of biologically diverse specimens. For this reason, we introduced a crowdsourcing program in which citizen scientists furnish soil samples from which new microbial isolates are procured. Illustrating the strength of this approach, we obtained a unique fungal metabolite, maximiscin, from a crowdsourced Alaskan soil sample. Maximiscin, which exhibits a putative combination of polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and shikimate pathway components, was identified as an inhibitor of UACC-62 melanoma cells (LC50=0.93 μM). The metabolite also exhibited efficacy in a xenograft mouse model. These results underscore the value of building cooperative relationships between research teams and citizen scientists to enrich drug discovery efforts.
Corrosion Resistance of Ca-Ni Added Weathering Steel in Marine Environment (1998)

Weathering steel has been widely used in many structures for its good corrosion resistance in unpainted condition, because a dense and tight rust layer naturally formed on the surface exhibits corrosion protectiveness It is, however, known that such a protective rust layer can not be created in the case of usage at seaside area. Thus, a Ca-Ni added weathering steel developed for applications to unpainted steel structures within the coastal area. Two types of outdoor exposure tests were carried out to evaluate its corrosion resistance; one is an ordinary exposure test and another is a sheltered exposure test. The results of these tests show that the amounts of corrosion loss are greater in the case of sheltered exposure tests than for ordinary exposure tests. Furthermore, the difference in the extents of corrosion in two types exposure tests is enhanced, as the amounts of chloride in the atmosphere increased. Larger extents of chloride ions are detected in the samples corroded in the sheltered condition than those in the ordinary test. It was found that Ca-Ni added weathering steel has a better corrosion resistance in such a severe environment, probably because alloying elements such as Ca, Ni contributed to prohibit the penetration of chloride ions to the interface between metal and rust layer.
Metformin and cancer therapy (2011)

The numerous in-vitro and in-vivo studies warrant the ongoing clinical trials, which should definitively help us to determine if metformin could be used in cancer therapy.
Identification of two regions of the human glucocorticoid receptor hormone binding domain that block activation. (1989)

The steroid-binding domain of the human glucocorticoid receptor has a dominant, negative influence over the activity of the remainder of the molecule. We have determined sequences within this domain that are responsible for this inhibition by creating truncations and internal deletions which remove part or all of the ligand-binding domain. Two apparently unrelated sequences within this region are shown to block the ability to stimulate transcription when fused to the carboxyl terminus of a functional, hormone-independent receptor derivative. These results support the possibility of two distinct protein-binding sites within the steroid-binding domain.
Sintering of Ultrafine Silicon Powder (1985)

The sintering behavior of compacts of ultrafine silicon powder (0.02 to 0.1 μm particle size) was investigated. Two sintering modes occur: normal sintering associated with densification and subnormal sintering without densification. The micro‐structure developed in normal sintering has a fine grain size (0.05 to 0.3 μm) and fine porosity; the grains contain stacking faults and twins. The microstructure developed in subnormal sintering exhibits larger grains (∼1 μm in size) and coarse pores. Green densities >42% of theoretical and temperatures >1100°C are required for densification. Densification follows an exponential time and temperature dependence with an activation energy of 470 kJ/mol, indicating bulk diffusion as the transport mechanism. Grain‐boundary diffusion is thought to be inhibited by grain‐boundary oxide films. The carbon phase‐separates into discrete amorphous regions and is thought to have little effect on sintering behavior.
Joint 2D-3D Breast Cancer Classification (2019)

Breast cancer is the malignant tumor that causes the highest number of cancer deaths in females. Digital mammograms (DM or 2D mammogram) and digital breast tomosynthesis (DBT or 3D mammogram) are the two types of mammography imagery that are used in clinical practice for breast cancer detection and diagnosis. Radiologists usually read both imaging modalities in combination; however, existing computer-aided diagnosis tools are designed using only one imaging modality. Inspired by clinical practice, we propose an innovative convolutional neural network (CNN) architecture for breast cancer classification, which uses both 2D and 3D mammograms, simultaneously. Our experiment shows that the proposed method significantly improves the performance of breast cancer classification. By assembling three CNN classifiers, the proposed model achieves 0.97 AUC, which is 34.72% higher than the methods using only one imaging modality.
Instrumental Activities of Daily Living as a Screening Tool for Cognitive Impairment and Dementia in Elderly Community Dwellers (1992)

The four IADL score could be incorporated into the screening procedure for dementia in elderly community dwellers.
Clinical significance of circulating galectins as colorectal cancer markers (2011)

The utility of CEA and CA19-9 as colorectal carcinoma (CRC) markers is limited and development of additional reliable markers is under investigation. We previously showed that galectin-1 is overexpressed in CRC tissues. If such a protein leaks into the peripheral circulation, it might constitute a tumor marker candidate. Here, we test the hypothesis that the levels of circulating galectins could reflect the presence of CRC and/or its progression state. We constructed sandwich ELISAs for galectin-1/-2/-3/-4/-7 and determined their plasma concentrations in 105 CRC patients and 100 healthy volunteers (control). Matched pair samples of 56 patients pre- and post-surgery were also subjected to ELISA analysis. Circulating levels of galectin-1/-3/-4 in CRC patients were significantly higher compared to those in controls. Galectin-1 and galectin-4 levels significantly decreased after surgery (P<0.01), and the level of galectin-4 in most patients fell below the cut-off value. The levels of circulating galectin-4 significantly increased as the tumor stage progressed (P<0.001), whereas those for galectin-1 were relatively high from an early stage. Combined use of galectin-4 with CEA and/or CA19-9 markedly increased the proportion of CRC patients who were positive for tumor markers (from 33.3 to 59.0% for CEA and from 17.1 to 51.4% for CA19-9). Our data show that galectin-4 may be a tumor marker for use in patient follow-up, while galectin-1 could be used for tumor screening. In particular, galectin-4 can be useful as a complementary marker when combined with CEA/CA19-9 to improve CRC follow-up.
Rheology of Block Copolypeptide Solutions:  Hydrogels with Tunable Properties (2004)

Amphiphilic block copolypeptides were prepared through transition-metal-mediated polymerization of amino acid N-carboxyanhydrides. In aqueous solution these materials form strong hydrogels at low concentrations. The self-assembly process that is responsible for gelation was investigated by measuring the rheological properties of the gels for a variety of molecular architectures: poly-l-lysine-b-poly-l-leucine diblock and poly-l-lysine-b-poly-l-leucine-b-poly-l-lysine triblock copolypeptides. Experiments showed that the rodlike helical secondary structure of enantiomerically pure poly-l-leucine blocks was instrumental for gelation at polypeptide concentrations as low as 0.25 wt %. The hydrophilic polyelectrolyte segments have stretched coil configurations and stabilize the twisted fibril assemblies by forming a corona around the hydrophobic core. The self-assembly of hydrophobic blocks is highly specific and sensitive to the chirality of the helices. It was found that mechanical properties of the gels can be tuned through the molecular architecture of the block copolypeptides and also by carefully mixing different polypeptides in solution.
Application-specific heterogeneous multiprocessor synthesis using differential-evolution (1998)

This paper presents an application-specific, heterogeneous multiprocessor synthesis system, named HeMPS, that combines a form of Evolutionary Computation known as Differential Evolution with a scheduling heuristic to search the design space efficiently. We demonstrate the effectiveness of our technique by comparing it to similar existing systems. The proposed strategy is shown to be faster than recent systems on large problems while providing equivalent or improved final solutions.
Extended Life-Span Conferred by Cotransporter Gene Mutations in <i>Drosophila</i> (2000)

Aging is genetically determined and environmentally modulated. In a study of longevity in the adult fruit fly, Drosophila melanogaster, we found that five independent P-element insertional mutations in a single gene resulted in a near doubling of the average adult life-span without a decline in fertility or physical activity. Sequence analysis revealed that the product of this gene, named Indy (for I'm not dead yet), is most closely related to a mammalian sodium dicarboxylate cotransporter-a membrane protein that transports Krebs cycle intermediates. Indy was most abundantly expressed in the fat body, midgut, and oenocytes: the principal sites of intermediary metabolism in the fly. Excision of the P element resulted in a reversion to normal life-span. These mutations may create a metabolic state that mimics caloric restriction, which has been shown to extend life-span.
Relative spectral response calibration of a spectrometer system for laser induced breakdown spectroscopy using the argon branching ratio method (2014)

This paper reports the use of the Ar branching ratio as an alternative means of calibrating the relative spectral response of a spectrometer/detector apparatus, with emphasis on its use in Laser Induced Breakdown Spectroscopy (LIBS) diagnostic experiments. The method is compared to the more conventional calibration routine using standard lamps. The argon method was implemented with an Ar-filled hollow cathode lamp and with a LIBS plasma in argon at different pressures. For the conventional calibration, a quartz tungsten halogen (QTH) lamp available in our laboratory has been used as a standard of spectral irradiance. The results obtained with the three methods are compared and discussed. It is shown that the spectral response data agree well with each other above 350 nm. At lower wavelengths, the data differ significantly. It is believed that this is due to the degradation of the calibration values of the lamp, which was not re-calibrated in a long time. It is concluded that the Ar-branching ratio method is a useful calibration technique for use with LIBS plasma diagnostic experiments.
Diagnosis and treatment of seborrheic dermatitis. (2015)

Seborrheic dermatitis is a common skin condition in infants, adolescents, and adults. The characteristic symptoms-scaling, erythema, and itching-occur most often on the scalp, face, chest, back, axilla, and groin. Seborrheic dermatitis is a clinical diagnosis based on the location and appearance of the lesions. The skin changes are thought to result from an inflammatory response to a common skin organism, Malassezia yeast. Treatment with antifungal agents such as topical ketoconazole is the mainstay of therapy for seborrheic dermatitis of the face and body. Because of possible adverse effects, anti-inflammatory agents such as topical corticosteroids and calcineurin inhibitors should be used only for short durations. Several over-the-counter shampoos are available for treatment of seborrheic dermatitis of the scalp, and patients should be directed to initiate therapy with one of these agents. Antifungal shampoos (long-term) and topical corticosteroids (short-term) can be used as second-line agents for treatment of scalp seborrheic dermatitis.
Modeling the Complete Otto Cycle-Preliminary Version (1977)

<div class="htmlview paragraph">A description is given of the equations and the computer program being developed to model the complete Otto cycle. The program incorporates such important features as: 1) heat transfer, 2) finite combustion rates, 3) complete chemical kinetics in the burned gas, 4) exhaust gas recirculation, and 5) manifold vacuum or supercharging. Changes in thermodynamic, kinetic and transport data as well as model parameters can be made without reprogramming. Preliminary calculations indicate that: 1) chemistry and heat transfer significantly affect composition and performance, 2) there seems to be a strong interaction among model parameters, and 3) a number of cycles must be calculated in order to obtain steady-state conditions.</div>