gebhart/patrepeval huggingface dataset:
Nanogel Engineered Polymeric Micelles for Drug Delivery (2008)

In the past few decades nanotechnology for drug delivery has attracted a great deal of attention. Nanogels under this category are sub-micron sized water swellable crosslinked structures of biocompatible hydrophillic polymers which have wide array of applications in drug delivery, biotechnology and biomedical field due to their nanosized structure with characteristics of nanoparticles and hydrogels. Nanogels are synthesized by emulsion polymerization, photopolymerization, pulse radiolysis, photo-Fenton reaction and physical self-assembly techniques. Nanogels are characterized by various microscopic techniques like scanning electron microscopy, atomic force microscopy and analytical techniques such as dynamic light scattering, zeta potential, fluorescence, nuclear magnetic resonance, size exclusion chromatography. Nanogels can trap novel nanobiomaterials and find application in delivery of proteins, peptides, gene delivery, insulin delivery, and as toxic scavengers. Thus nanogels can act as a carrier as well as sustained release can be achieved by designing responsive nanogels such as pH, thermo, photo or magneto-responsive nanogels. Thus the article focuses on the synthesis, characterization and applications of nanogels. Keywords: Nanogels, biocompatible, emulsion polymerization, scanning electron microscopy, proteins and peptide, toxic scavenger
Bacterial display enables efficient and quantitative peptide affinity maturation (2009)

A quantitative screening method was developed to enable isolation and affinity maturation of peptide ligands specific for a given target from peptide libraries displayed on the outer surface of Escherichia coli using multi-parameter flow cytometry. From a large, random 15-mer peptide library, screening identified a core motif of W-E/D-W-E/D that conferred binding to vascular endothelial growth factor (VEGF). One cycle of affinity maturation resulted in the identification of several families of VEGF-binding peptides having distinct consensus sequences, from which a preferred disulfide constraint emerged. In the second affinity maturation cycle, high affinity peptides were favored by the addition of a decoy protein that bound an adjacent epitope on the display scaffold. The decoy apparently reduced rebinding or avidity effects, and the resulting peptides exhibited consensus at 12 of 19 amino acid positions. Peptides identified and affinity matured using bacterial display were remarkably similar to the best affinity matured using phage display and exhibited comparable dissociation constants (within 2-fold; K(D) = 4.7 x 10(-7) M). Screening of bacterial-displayed peptide libraries using cytometry enabled optimization of screening conditions to favor affinity and specificity and rapid clonal characterization. Bacterial display thus provides a new quantitative tool for the discovery and evolutionary optimization of protein-specific peptide ligands.
Activation of Receptor Activator of NF-κB Ligand Gene Expression by 1,25-Dihydroxyvitamin D3 Is Mediated through Multiple Long-Range Enhancers (2006)

RANKL is a tumor necrosis factor (TNF)-like factor secreted by mesenchymal cells, osteoblast derivatives, and T cells that is essential for osteoclastogenesis. In osteoblasts, RANKL expression is regulated by two major calcemic hormones, 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] and parathyroid hormone (PTH), as well as by several inflammatory/osteoclastogenic cytokines; the molecular mechanisms for this regulation are unclear. To identify such mechanisms, we screened a DNA microarray which tiled across the entire mouse RankL gene locus at a 50-bp resolution using chromatin immunoprecipitation (ChIP)-derived DNA precipitated with antibodies to the vitamin D receptor (VDR) and the retinoid X receptor (RXR). Five sites of dimer interaction were observed on the RankL gene centered at 16, 22, 60, 69, and 76 kb upstream of the TSS. These regions contained binding sites for not only VDR and RXR, but also the glucocorticoid receptor (GR). The most distant of these regions, termed the distal control region (RL-DCR), conferred both VDR-dependent 1,25(OH)(2)D(3) and GR-dependent glucocorticoid (GC) responses. We mapped these activities to an unusual but functionally active vitamin D response element and to several potential GC response elements located over a more extensive region within the RL-DCR. An evolutionarily conserved region within the human RANKL gene contained a similar vitamin D response element and exhibited an equivalent behavior. Importantly, hormonal activation of the RankL gene was also associated with chromatin modification and RNA polymerase II recruitment. Our studies demonstrate that regulation of RankL gene expression by 1,25(OH)(2)D(3) is complex and mediated by at least five distal regions, one of which contains a specific element capable of mediating direct transcriptional activation.
RETRACTED ARTICLE: miR-663 attenuates tumor growth and invasiveness by targeting eEF1A2 in pancreatic cancer (2015)

miR-663 attenuated the proliferation and invasion of pancreatic cells both in vitro and in vivo by directly targeting eEF1A2. miR-663 and eEF1A2 might be potential targets for the treatment of pancreatic cancer in the future.
IL-2 induces expression of serine protease enzymes and genes in natural killer and nonspecific T killer cells. (1989)

The expression of serine protease genes was examined in murine NK cells that were purified by panning spleen cells with PMA. Although unstimulated NK cells were cytolytic, they were found not to express the C11 (chymotrypsin-like) mRNA. Culturing these cells in IL-2 (500 to 800 U/ml) for 5 to 7 days induced both the lytic activities and the protease enzymes by 20- to 30-fold. Concomitant to these activation events, the total steady state mRNA of both C11 and HF (trypsin-like) genes were also elevated. The activation of lysis, serine protease enzymes, and C11 and HF mRNA all peaked around day 5 in culture and was dose dependent. In order to exclude the possibility that PMA synergizes with IL-2 in this system, spleen cells from SCID mice, which contained mainly NK cells, were cultured under the same conditions (800 U/ml IL-2, with or without PMA) and PMA did not appear to enhance the expression of these mRNA. Similarly, IL-2 also induced the lytic activities, enzyme levels, and mRNA in the non-Ag-specific T killer cells isolated from spleens of normal mice. Lytic activity of T killer cells was not as high as the NK cells, however, the addition of PHA into the lytic assay resulted in enhanced lysis comparable to that of NK cells. These results showed that lytic activity increased along with protease enzyme levels and mRNA expression in both NK and resting T cells. Therefore, elevated levels of the protease enzymes could be one mechanism involved in optimal lytic activity of IL-2-induced lymphokine activated killer cells.
Structure-Based Discovery of Ligands Targeted to the RNA Double Helix (1997)

Ligands capable of specific recognition of RNA structures are of interest in terms of the principles of molecular recognition as well as potential chemotherapeutic applications. We have approached the problem of identifying small molecules with binding specificity for the RNA double helix through application of the DOCK program [Kuntz, I. D., Meng, E. C., and Shoichet, B. K. (1994) Acc. Chem. Res. 27, 117-123], a structure-based method for drug discovery. A series of lead compounds was generated through a database search for ligands with shape complementarity to the RNA deep major groove. Compounds were then evaluated with regard to their fit into the minor groove of B DNA. Those compounds predicted to have an optimal fit to the RNA groove and strong discrimination against DNA were examined experimentally. Of the 11 compounds tested, 3, all aminoglycosides, exhibited pronounced stabilization of RNA duplexes against thermal denaturation with only marginal effects on DNA duplexes. One compound, lividomycin, was examined further, and shown to facilitate the ethanol-induced B to A transition in calf thymus DNA. Fluorine NMR solvent isotope shift measurements on RNA duplexes containing 5-fluorouracil provided evidence that lividomycin binds in the RNA major groove. Taken together, these results indicate that lividomycin recognizes the general features of the A conformation of nucleic acids through deep groove binding, confirming the predictions of our DOCK analysis. This approach may be of general utility for identifying ligands possessing specificity for additional RNA structures as well as other nucleic acid structural motifs.
Narrow band laser-generated surface acoustic waves using a formed source in the ablative regime (2003)

A narrow band laser-generated acoustic signal was created using a 4-element lenticular array. This arrangement of the array produces an acoustical signal with frequency content that is compatible with the response of a noncontact and remote broadband receiver, such as a capacitive air-coupled transducer. To support the experimental observations, a simplified concept is presented to explain the effect of a line array source on the frequency content of a surface acoustic wave. The analytical model solution for the wave front shape is derived from the point load solution of Lamb's problem that represents the displacement of a surface acoustic wave generated by an ablative line array. The distribution function, which was used for the model to represent the laser light energy, was tailored to depict the actual energy distribution that illuminates the lenticular array. Filtering functions are applied to the resultant surface displacement function to retain frequencies similar to those detected by the broadband 50 kHz-2.25 MHz receiver. The theoretical model showed good agreement with experimental results.
Regulation of Gene Expression in Hippocampal Neurons by Distinct Calcium Signaling Pathways (1993)

Calcium ions (Ca2+) act as an intracellular second messenger and can enter neurons through various ion channels. Influx of Ca2+ through distinct types of Ca2+ channels may differentially activate biochemical processes. N-Methyl-D-aspartate (NMDA) receptors and L-type Ca2+ channels, two major sites of Ca2+ entry into hippocampal neurons, were found to transmit signals to the nucleus and regulated gene transcription through two distinct Ca2+ signaling pathways. Activation of the multifunctional Ca(2+)-calmodulin-dependent protein kinase (CaM kinase) was evoked by stimulation of either NMDA receptors or L-type Ca2+ channels; however, activation of CaM kinase appeared to be critical only for propagating the L-type Ca2+ channel signal to the nucleus. Also, the NMDA receptor and L-type Ca2+ channel pathways activated transcription by means of different cis-acting regulatory elements in the c-fos promoter. These results indicate that Ca2+, depending on its mode of entry into neurons, can activate two distinct signaling pathways. Differential signal processing may provide a mechanism by which Ca2+ controls diverse cellular functions.
A New Aliphatic Amino Prodrug System for the Delivery of Small Molecules and Proteins Utilizing Novel PEG Derivatives (2003)

A new amino PEG prodrug system, based entirely on aliphatic structures, has been designed using ester derivatives easily synthesized from N-modified bis-N-2-hydroxyethylglycinamides. Hydrolysis of the various promoiety bonds, in vivo, regenerated amine in a predictable manner. Thus, a novel new methodology for controlled release of amino-containing drugs, peptides, and proteins has been accomplished. This work demonstrates the usefulness of a PEG prodrug strategy that results in solubilization of insoluble amino-containing drugs and provides prodrugs with relatively long circulating half-lives. It can be appreciated that this novel system should also be applicable for nonpolymer-containing prodrugs as well.
FlowNet 2.0: Evolution of Optical Flow Estimation with Deep Networks (2017)

The FlowNet demonstrated that optical flow estimation can be cast as a learning problem. However, the state of the art with regard to the quality of the flow has still been defined by traditional methods. Particularly on small displacements and real-world data, FlowNet cannot compete with variational methods. In this paper, we advance the concept of end-to-end learning of optical flow and make it work really well. The large improvements in quality and speed are caused by three major contributions: first, we focus on the training data and show that the schedule of presenting data during training is very important. Second, we develop a stacked architecture that includes warping of the second image with intermediate optical flow. Third, we elaborate on small displacements by introducing a subnetwork specializing on small motions. FlowNet 2.0 is only marginally slower than the original FlowNet but decreases the estimation error by more than 50%. It performs on par with state-of-the-art methods, while running at interactive frame rates. Moreover, we present faster variants that allow optical flow computation at up to 140fps with accuracy matching the original FlowNet.
<title>Two-photon geometric optical imaging and quantum cryptoFAX</title> (1996)

A nonlocal two-photon quantum effect which surprisingly shows some features analogous to geometrical imaging optics is observed. The remote transfer of two-dimensional analog information with a high degree of security (quantum 'cryptoFAX') is demonstrated.
Use of small RNA as antiaging cosmeceuticals. (2014)

Over the past two decades, RNA interference (RNAi) has achieved great improvements in medicine, which has benefited the development of innovative cosmeceutical products, particular, to antiaging cosmeceuticals. A variety of ongoing research has tried to employ small RNAs-small interference RNA and microRNA as new cosmeceutical ingredients. Furthermore, several skin care companies have released new small RNA products in cosmetic market. In this review, we will describe the latest and most advanced approaches and strategies of using small RNA as antiaging cosmetics, including investigations on aging-related genes that small RNA target, method of delivering them, and challenges in the development of RNAi-based therapeutics for skin care cosmeceuticals. It is certain that advancement in this direction will evolve a new landscape for innovative antiaging cosmeceuticals.
Generation of Anti-Insulin-Like Growth Factor-Binding Protein-Related Protein 1 (IGFBP-rP1/MAC25) Monoclonal Antibodies and Immunoassay: Quantification of IGFBP-rP1 in Human Serum and Distribution in Human Fluids and Tissues (2003)

The IGF-binding protein (IGFBP)-related proteins (rPs) are a group of recently described cysteine-rich proteins that share significant amino-terminal structural similarity with the conventional IGFBPs. IGFBP-rP1 (also known as MAC25/angiomodulin/prostacyclin-stimulating factor and T1A12), regulates cellular proliferation, adhesion, and angiogenesis and stimulates prostacyclin synthesis. We characterized new monoclonal antibodies generated against IGFBP-rP1 and have used them to study the distribution of IGFBP-rP1 in human biological fluids and tissues. Additionally, we have developed a noncompetitive sandwich-type immunoassay to quantitate the concentrations of IGFBP-rP1 in human serum. IGFBP-rP1 was readily detectable in serum, urine, amniotic fluid, and cerebrospinal fluid by immunoblot analysis. Evaluation of the newly developed immunoassay demonstrated acceptable analytical performance, with a detection limit of 0.7 micro g/liter, a dynamic range of 3.1-100 micro g/liter, and intra- and interassay coefficients of variation of 2.5-6.8% and 3.1-6.4% at approximately 24-85 ng/ml IGFBP-rP-1, respectively. No significant cross-reactivity with IGFBP-1-6 was observed. In random normal human adult sera (n = 37), the median IGFBP-rP1 was 21.0 micro g/liter, and values did not correlate with levels of IGF-I (r = 0.085, P = 0.61), IGF-II (r = 0.051, P = 0.75), or IGFBP-3 (r = 0.061, P = 0.74). The monoclonal anti-IGFBP-rP1 antibodies also readily detected IGFBP-rP1 expression in human tissue sections, with preferential expression of IGFBP-rP1 in the microvascular endothelium associated with tumorigenesis. In summary, using newly developed IGFBP-rP1 monoclonal antibodies, we confirm the presence of IGFBP-rP1 in the major human body fluids, provide quantitative normative data on the concentrations of IGFBP-rP1 in human serum, and show preferential expression of IGFBP-rP1 in the microvascular endothelium associated with tumorigenesis. The use of these novel IGFBP-rP1 detection tools should prove useful in the elucidation of the biological role(s) of this protein.
A New Enzyme Mixture to Increase the Yield and Transplant Rate of Autologous and Allogeneic Human Islet Products (2012)

A NEM composed of ChNP with CIzyme high intact C1 collagenase recovers higher islet yield from deceased and pancreatitis pancreases while retaining islet quality and function.
In vitro mutagenesis of a circular DNA molecule by using synthetic restriction sites. (1978)

A method for mutagenizing circular DNA molecules has been developed that uses synthetic oligodeoxynucleotide restriction sites as mutagens. A single synthetic restriction site is introduced at random by cleaving circular DNA with a nonspecific double-strand endonuclease. The restriction site is then ligated to the ends and the molecule is subsequently recircularized. These small additions to the genome are mapped by digestion with the appropriate restriction enzyme. Rearrangements such as duplications and deletions can be engineered at will by using the added restriction sites. This technique has been used to produce a fine-structure map of RSF1050, a ColE1 derivative, 60% of which is a transposable DNA sequence encoding the TEM beta-lactamase (Tn3). A subset of the mutations, mapping within a narrow region of Tn3, result in an increased frequency of Tn3 transposition; mutations in other regions abolish transposition entirely.
Transgenic Mice Expressing Human Fibroblast Growth Factor-19 Display Increased Metabolic Rate and Decreased Adiposity (2002)

The fibroblast growth factors (FGFs), and the corresponding receptors, are implicated in more than just the regulation of epithelial cell proliferation and differentiation. Specifically, FGF23 is a regulator of serum inorganic phosphate levels, and mice deficient in FGF receptor-4 have altered cholesterol metabolism. The recently described FGF19 is unusual in that it is nonmitogenic and appears to interact only with FGF receptor-4. Here, we report that FGF19 transgenic mice had a significant and specific reduction in fat mass that resulted from an increase in energy expenditure. Further, the FGF19 transgenic mice did not become obese or diabetic on a high fat diet. The FGF19 transgenic mice had increased brown adipose tissue mass and decreased liver expression of acetyl coenzyme A carboxylase 2, providing two mechanisms by which FGF19 may increase energy expenditure. Consistent with the reduction in expression of acetyl CoA carboxylase 2, liver triglyceride levels were reduced.
The integration of signaling and the spatial organization of the T cell synapse (2012)

Engagement of the T cell antigen receptor (TCR) triggers signaling pathways that lead to T cell selection, differentiation and clonal expansion. Superimposed onto the biochemical network is a spatial organization that describes individual receptor molecules, dimers, oligomers and higher order structures. Here we discuss recent findings and new concepts that may regulate TCR organization in naïve and memory T cells. A key question that has emerged is how antigen-TCR interactions encode spatial information to direct T cell activation and differentiation. Single molecule super-resolution microscopy may become an important tool in decoding receptor organization at the molecular level.
A fundamental limit on the accuracy of speckle signal alignment (1994)

Signal alignment is performed in phase aberration correction and measurement, tissue elasticity estimation, and tissue and blood velocity estimation. The performance of all these techniques is limited by errors in the alignment of signals received from speckle generating targets. We have derived an analytical expression based on the Cramer-Rao lower bound which predicts the magnitude of jitter errors resulting from the alignment of radio frequency speckle data. The expression includes the effects of finite length samples of data, signal decorrelation, electronic noise, signal bandwidth, and center frequency. This expression indicates that signal decorrelation is a significant source of jitter for many ultrasound applications
Motivação: uma breve revisão de conceitos e aplicações (2005)

O assunto relacionado a motivacao pessoal tem alcancado grande importância atualmente. Em razao deste destaque encontra-se na literatura os mais diversos conceitos e aplicacoes sobre motivacao. O objetivo deste texto e de apresentar brevemente alguns conceitos e aplicacoes para motivar pessoas a praticar atividade fisica durante um longo periodo de tempo. Portanto, espera-se que este artigo sirva como uma especie de guia com algumas abordagens sobre motivacao, motivos, teorias motivacionais e suas aplicacoes para quaisquer pessoas que sejam interessados no assunto ou estejam estudando o tema.
DNA Binding Compounds. V. Synthesis and Characterization of Boron Containing Bibenzimidazoles Related to the DNA Minor Groove Binder, Hoechst-33258 (1994)

The synthesis and characterization of four novel boron-containing bibenzimidazoles related to the DNA minor groove binder Hoechst 33258 are reported. Such compounds, particularly their 1°B-enriched forms, have potential as agents for boron neutron capture therapy which is used in the treatment of cancers.
Luminescence centers in calcium co-doped LSO:Ce single crystals (2009)

Experimental studies of LSO:Ce crystals co-doped with various concentrations of Ca are presented. Photoluminescence decay time, excitation and emission spectra, thermal response and X-ray radioluminescence are investigated as a function of Ca concentration. Experimental data show Ca co-doping does not alter the energy level structure of either Ce1 or Ce2, but reduces the relative population of Ce2 to Ce1. Thus, the luminescence from Ce2 is suppressed, which contributes to the fast scintillation decay of Ca co-doped LSO:Ce.
Image segmentation scale parameter optimization and land cover classification using the Random Forest algorithm (2010)

This paper describes an approach to using the Random Forest classification algorithm to quantitatively evaluate a range of potential image segmentation scale alternatives in order to identify the segmentation scale(s) that best predict land cover classes of interest. The image segmentation scale selection process was used to identify three critical image object scales that when combined produced an optimal level of land cover classification accuracy. Following segmentation scale optimization, the Random Forest classifier was then used to assign land cover classes to 11 scenes of SPOT satellite imagery in North and South Dakota with an average overall accuracy of 85.2 percent.