gebhart/patrepeval huggingface dataset:
Oligodeoxynucleotide 5mers containing a 5'-CpG induce apoptosis through a mitochondrial mechanism in T lymphocytic leukaemia cells (2000)

A chimeric methylphosphonodiester/phosphodiester 15mer oligodeoxynucleotide of randomly selected sequence was observed to rapidly induce apoptosis in MOLT-4 and Jurkat E6 T lymphocytic leukaemia cells following intracytoplasmic delivery. A series of further methylphosphonate substitutions and mutations and truncations of the oligodeoxynucleotide served to establish that the phosphodiester-linked sequence CGGTA present in the 15mer was responsible for this biological activity. End-protected CpG oligodeoxy-nucleotide 5mers of sequence type CGNNN exhibited a range of apoptosis-inducing potencies, with CGTTA being the most active. The latter was shown to significantly reduce the rate of RNA synthesis in MOLT-4 cells within 1 h; DNA laddering and redistribution of phosphatidylserine to the outer surface of the plasma membrane were marked by 160 min and mitochondrial transmembrane potential collapsed over roughly the same time scale. Pro-caspase 8 was reduced within 130 min and the proteolytically activated caspase 8 substrate Bid was also down by this time, implicating release of cytochrome c from mitochondria by the active 15 kDa fragment of Bid. Substantial proteolytic activation of pro-caspase 3 was relatively delayed. These findings support a mitochondrial amplification mechanism for apoptosis triggered by CpG 5mers.
Surface acid proteinase (gp63) of Leishmania mexicana (1989)

Acid proteinase activity is associated with the major surface glycoprotein (gp63) of both extracellular promastigotes and intracellular amastigotes of the parasitic protozoan, Leishmania mexicana. The enzyme purified by monoclonal affinity chromatography from promastigotes is strongly inhibited by metal ion chelators, which is reversible by the addition of Zn(II). This proteinase loses its activity after dialysis against 1,10-phenanthroline. The apoenzyme thus prepared is reactivated substantially by Zn(II) and partially by Cu(II), Cd(II), Co(II), or Ni(II). From the recently published structure of the gene encoding gp63, we identify hitherto unrecognized sequences, which can be aligned to the consensus zinc-binding sites of other known metalloproteinases. Anti-gp63 polyclonal antibodies, but not the monoclonals, precipitate similar molecules from amastigotes. These molecules differ slightly from gp63 in electrophoretic mobility but have similar endopeptidase activity. Phagolysosomal degradation by macrophages of proteins entrapped in liposomes is prevented by coating them with native gp63. This protection is lost with heat denaturation of gp63 to kill its enzymatic activity. The proteolytic activity of the metalloenzyme on the surface of these parasites may thus protect their membrane from cytolytic damages during their survival, differentiation, and multiplication in the phagolysosomes of macrophages.
Electrical properties of shallow p+-n junction using boron-doped Si1−xGex layer deposited by ultrahigh vacuum chemical molecular epitaxy (2001)

Strained boron-doped Si1−xGex layers with different Ge mole fractions were selectively deposited by ultrahigh vacuum chemical molecular epitaxy to form shallow p+-n junction suitable for raised source/drain metal–oxide–semiconductor field effect transistor applications. Detailed electrical characterizations were performed. Our results show that the reverse leakage current could be optimized by a rapid thermal annealing at 950 °C for 20 s, and a near perfect forward ideality factor (i.e., &amp;lt;1.01) is obtained for the p+-n Si1−xGex/Si junction. By analyzing the periphery and area leakage current components of p+-n Si1−xGex/Si junctions with various perimeter lengths and areas, the degree of misfit dislocations and undercut effect were studied. The specific contact resistance was found to decrease as Ge mole fraction increases. Junction depth measurements also show that the junction depth decreases monotonically with increasing Ge mole fraction. The reduced B diffusion constant is attributed to the increasing Ge gradient in the transition region.
Enhanced spatial modulation with multiple constellations (2014)

Spatial modulation (SM) has recently drawn a great deal of attention, particularly due to the low complexity that it promises for both the transmitter and the receiver sides. However, this technique has a significant spectral efficiency loss with respect to spatial multiplexing (SMX) with the same number of transmit (Tx) antennas, and when the modulation order is increased to achieve the same spectral efficiency, it loses in terms of the bit error rate (BER). In this paper, a new type of SM (referred to as Enhanced SM) is proposed which increases the number of bits transmitted per channel use compared to conventional SM. Note that conventional MEMO techniques including SMX and SM employ a fixed signal constellation. In our proposed technique, some information bits select not only the index(es) of the active antenna(s), but also the constellations to be transmitted from each of them. Both the closed-form analysis and the numerical results demonstrate that the proposed technique achieves better performance than conventional SM and that in most cases it also outperforms SMX.
Image retrieval using multiple evidence ranking (2004)

The World Wide Web is the largest publicly available image repository and a natural source of attention. An immediate consequence is that searching for images on the Web has become a current and important task. To search for images of interest, the most direct approach is keyword-based searching. However, since images on the Web are poorly labeled, direct application of standard keyword-based image searching techniques frequently yields poor results. We propose a comprehensive solution to this problem. In our approach, multiple sources of evidence related to the images are considered. To allow combining these distinct sources of evidence, we introduce an image retrieval model based on Bayesian belief networks. To evaluate our approach, we perform experiments on a reference collection composed of 54000 Web images. Our results indicate that retrieval using an image surrounding text passages is as effective as standard retrieval based on HTML tags. This is an interesting result because current image search engines in the Web usually do not take text passages into consideration. Most important, according to our results, the combination of information derived from text passages with information derived from HTML tags leads to improved retrieval, with relative gains in average precision figures of roughly 50 percent, when compared to the results obtained by the use of each source of evidence in isolation.
In vitro activity of novel sulphonic derivatives of distamicyn A (1992)

Solid tumor growth can be modulated through inhibition of vascularization elicited by angiogenic factors. With the objective to complex these factors, new derivatives of distamycin A were synthesized and evaluated in vitro [1] and in vivo for their ability, after i.v. administration, to inhibit bFGF-induced vascularization and the growth of M5076 murine reticulosarcoma implanted i.m. The tested compounds were able to block angiogenesis with inhibition values ranging between 70-100%. Moreover, they were found to be capable of inducing tumor inhibition with values ranging between 40% and 95% at non-toxic doses.
In vivo cytometry: A spectrum of possibilities (2006)

The results demonstrate that advanced optical imaging can detect and localize cellular signatures of cancer in real-time, in vivo, without the use of contrast agents, in animals and humans. This is an important step towards tight spatio-temporal coupling between such detection and clinical intervention.
Voltage-based maximum power point tracking control of PV system (2002)

Photovoltaic (PV) generators exhibit nonlinear v-i characteristics and maximum power (MP) points that vary with solar insulation. An intermediate converter can therefore increase efficiency by matching the PV system to the load and by operating the solar cell arrays (SCAs) at their maximum power point. An MP point tracking algorithm is developed using only SCA voltage information thus leading to current sensorless tracking control. The inadequacy of a boost converter for array voltage based MP point control is experimentally verified and an improved converter system is proposed. The proposed converter system results in low ripple content, which improves the array performance and hence a lower value of capacitance is sufficient on the solar array side. Simplified mathematical expressions for a PV source are derived. A signal flow graph is employed for modeling the converter system. Current sensorless peak power tracking effectiveness is demonstrated through simulation results. Experimental results are presented to validate the proposed method.
Frequency invariant beamforming in subbands (2005)

In this paper, two subband implementations of a frequency invariant beamformer (FIB) are studied. In the first structure, the received array signals are split into subbands and an FIB is operated in each of the corresponding decimated subbands, with a potential of achieving a lower computational complexity. As the spatio-temporal distribution of the subband signals is different from the original fullband signal, a modified design method of the FIB is proposed. Based on the subband implementation, we then change the sensor spacings of different subband signals so that lower frequency bands have a larger spacing, which results in a class of FIBs with scaled aperture with improved performance in lower frequencies. Several design examples are given to show the performance of our new structures.
Unfolded state of polyalanine is a segmented polyproline II helix (2004)

Definition of the unfolded state of proteins is essential for understanding their stability and folding on biological timescales. Here, we find that under near physiological conditions the configurational ensemble of the unfolded state of the simplest protein structure, polyalanine alpha-helix, cannot be described by the commonly used Flory random coil model, in which configurational probabilities are derived from conformational preferences of individual residues. We utilize novel effectively ergodic sampling algorithms in the presence of explicit aqueous solvation, and observe water-mediated formation of polyproline II helical (P(II)) structure in the natively unfolded state of polyalanine, and its facilitation of alpha-helix formation in longer peptides. The segmented P(II) helical coil preorganizes the unfolded state ensemble for folding pathway entry by reducing the conformational space available to the diffusive search. Thus, as much as half of the folding search in polyalanine is accomplished by preorganization of the unfolded state.
Entry of adenovirus 2 into HeLa cells (1984)

Adenovirus 2 (Ad2) uncoating was analyzed as the destabilization of virions which renders the parental genome sensitive to DNase treatment. This event demonstrated a strong temperature dependence, and an Arrhenius plot of initial uncoating rates revealed an inflection point at around 16 degrees C. Activation energies of 331 kJ/mol below and 88 kJ/mol above this temperature were obtained for the uncoating process. Penetration of Ad2 through the plasma membrane was completely inhibited by sodium azide, whereas uncoating was only slightly influenced. This indicated that uncoating had already taken place at the outside of the plasma membrane. Incubations of Ad2 with isolated plasma membranes and cell homogenates showed that intact and metabolizing cells were required for uncoating. We further suggest, based on the inhibitory patterns of EDTA, EGTA, dansylcadaverine, and dithiothreitol, that this destabilization of virions follows upon reorganization in the plasma membrane. In the electron microscope the involvement of coated vesicles was shown for the initial uptake of virions, possibly followed by the engagement of acidic vesicles as judged from the effects of lysosomotropic agents on gene expression. The vectorial transport of virions from the plasma membrane to the nucleus was not affected by reagents interfering with the cytoskeletal system. Consequently, we propose that Ad2 virions are internalized by adsorptive endocytosis.
Mucosal IFN-gamma gene transfer inhibits pulmonary allergic responses in mice (1996)

Th2 cytokines are associated with the airway inflammation and hyperreactivity in allergic asthma and are potential targets for developing novel therapies. The efficacy of a mucosal cytokine-gene transfer approach was examined in a mouse model for allergic asthma. We showed first that mucosal IFN-gamma gene transfer results in a significant expression of IFN-gamma in the pulmonary epithelium. Significantly, this approach inhibits both Ag- and Th2-cell-induced pulmonary eosinophilia and airway hyperreactivity. These findings suggest that mucosal IFN-gamma gene transfer is effective in modulating pulmonary allergic responses and provides a basis for developing a novel therapeutic approach.
The divergence of reinforcement learning algorithms with value-iteration and function approximation (2012)

This paper gives specific divergence examples of value-iteration for several major Reinforcement Learning and Adaptive Dynamic Programming algorithms, when using a function approximator for the value function. These divergence examples differ from previous divergence examples in the literature, in that they are applicable for a greedy policy, i.e. in a “value iteration” scenario. Perhaps surprisingly, with a greedy policy, it is also possible to get divergence for the algorithms TD(1) and Sarsa(1). In addition to these divergences, we also achieve divergence for the Adaptive Dynamic Programming algorithms HDP, DHP and GDHP.
Conformational stability, folding, and ligand-binding affinity of single-chain Fv immunoglobulin fragments expressed in Escherichia coli (1991)

A fluorescein-binding single-chain Fv (scFv) was chosen as a model for the study of the physicochemical parameters associated with synthetic IgG fragments. Three such scFv proteins were designed from the primary sequences of one anti-fluorescyl monoclonal antibody (Mab 4.4.20). These were constructed with varying-length interdomain peptide linkers of between 12 and 25 residues, expressed in Escherichia coli, and the protein folding, stability, and antigen-binding characteristics were assessed. Efficient renaturation could be accomplished in vitro to yield approximately 26 mg of active scFv/L of fermentation. Scatchard analysis for fluorescein ligand binding revealed that the scFv designs come within 2-fold of the Ka = 1.99 (+/- 0.18) x 10(9) observed for the parental 4.4.20 Fab and have identical stoichiometries (n approximately 0.99). Reversible solvent denaturation studies demonstrated that the unfolding/refolding equilibria for the scFv proteins can be fit to a simple two-state model and that two of the scFv designs were found to be slightly more stable than single IgG domains (VL and CL) when assessed in terms of the free energy of unfolding, delta Gon-u, or nearly identical to other multiple domain immunoglobulin proteins such as light chains and Fab's when relative transition midpoints, Cm, are compared. Linkers which conferred conformational flexibility beyond the minimally required length of 12 residues were found to have a stabilizing effect. By these criteria of ligand-binding function and protein stability, the scFv proteins were found to be bona fide minimal replicas of their parental IgG molecules.
βig-h3: A Transforming Growth Factor-β-Responsive Gene Encoding a Secreted Protein That Inhibits Cell Attachment In Vitro and Suppresses the Growth of CHO Cells in Nude Mice (1994)

beta ig-h3 is a novel gene first discovered by differential screening of a cDNA library made from A549 human lung adenocarcinoma cells treated with transforming growth factor-beta 1 (TGF-beta 1). It encodes a 683-amino-acid protein containing a secretory signal sequence and four homologous internal domains. Here we show that treatment of several types of cells, including human melanoma cells, human mammary epithelial cells, human keratinocytes, and human fibroblasts, with TGF-beta resulted in a significant increase in beta ig-h3 RNA. A portion of the beta ig-h3 coding sequence was expressed in bacteria, and antisera against the bacterially produced protein was raised in rabbits. This antisera was used to demonstrate that several cell lines secreted a 68-kD beta IG-H3 protein after treatment with TGF-beta. Transfection of beta IG-H3 expression plasmids into Chinese hamster ovary (CHO) cells led to a marked decrease in the ability of these cells to form tumors in nude mice. The beta IG-H3 protein was purified from media conditioned by recombinant CHO cells, characterized by immunoblotting and protein sequencing and shown to function in an anti-adhesion assay in that it inhibited the attachment of A549, HeLa, and WI-38 cells to plastic in serum-free media. Sequencing of cDNA clones encoding murine beta ig-H3 indicated 90.6% conservation at the amino acid level between the murine and human proteins. Finally, the beta ig-h3 gene was localized to human chromosome 5q31, a region frequently deleted in preleukemic myelodysplasia and leukemia. The corresponding mouse beta ig-h3 gene was mapped to mouse chromosome 13 region B to C1, which confirms a region of conservation on human chromosome 5 and mouse chromosome 13. We suggest that this protein be named p68 beta ig-h3.
Neuromorphic implementation of orientation hypercolumns (2005)

Neurons in the mammalian primary visual cortex are selective along multiple stimulus dimensions, including retinal position, spatial frequency, and orientation. Neurons tuned to different stimulus features but the same retinal position are grouped into retinotopic arrays of hypercolumns. This paper describes a neuromorphic implementation of orientation hypercolumns, which consists of a single silicon retina feeding multiple chips, each of which contains an array of neurons tuned to the same orientation and spatial frequency, but different retinal locations. All chips operate in continuous time, and communicate with each other using spikes transmitted by the address-event representation protocol. This system is modular in the sense that orientation coverage can be increased simply by adding more chips, and expandable in the sense that its output can be used to construct neurons tuned to other stimulus dimensions. We present measured results from the system, demonstrating neuronal selectivity along position, spatial frequency and orientation. We also demonstrate that the system supports recurrent feedback between neurons within one hypercolumn, even though they reside on different chips. The measured results from the system are in excellent concordance with theoretical predictions.
Catheter-based renal denervation for treatment of patients with treatment-resistant hypertension: 36 month results from the SYMPLICITY HTN-2 randomized clinical trial (2014)

The aim of this study was to determine long-term results of renal artery denervation for treatment of treatment-resistant hypertension in the SYMPLICITY HTN-2 study.
Fibronectin matrix polymerization regulates small airway epithelial cell migration (2003)

The continuous conversion of soluble fibronectin into extracellular matrix fibrils occurs through a dynamic, cell-dependent process. As the extracellular matrix is assembled, changes in the conformation of matrix proteins may expose biologically active, matricryptic sites that alter cell behavior. In this study, an in vitro model of wound healing was used to determine the role of matrix fibronectin in airway epithelial cell motility. Our findings indicate that, under basal conditions, small airway epithelial cell (SAEC) migration requires active fibronectin matrix polymerization. Furthermore, SAEC migration is increased significantly by the interaction of cells with a recombinant construct containing fibronectin's matricryptic III-1 site. In contrast, addition of increasing amounts of fibronectin to SAECs significantly decreased the rate of cell migration. This fibronectin-induced inhibition of cell migration was overcome by blocking excess fibronectin matrix deposition. These data indicate that SAEC migration is regulated in a biphasic manner by the polymerization of fibronectin in the extracellular matrix and suggest a stimulatory role for fibronectin's matricryptic III-1 site in cell motility.
Identification of a Novel Protein Kinase A Anchoring Protein That Binds Both Type I and Type II Regulatory Subunits (1997)

Compartmentalization of cAMP-dependent protein kinase is achieved in part by interaction with A-kinase anchoring proteins (AKAPs). All of the anchoring proteins identified previously target the kinase by tethering the type II regulatory subunit. Here we report the cloning and characterization of a novel anchoring protein, D-AKAP1, that interacts with the N terminus of both type I and type II regulatory subunits. A novel cDNA encoding a 125-amino acid fragment of D-AKAP1 was isolated from a two-hybrid screen and shown to interact specifically with the type I regulatory subunit. Although a single message of 3.8 kilobase pairs was detected for D-AKAP1 in all embryonic stages and in most adult tissues, cDNA cloning revealed the possibility of at least four splice variants. All four isoforms contain a core of 526 amino acids, which includes the R binding fragment, and may be expressed in a tissue-specific manner. This core sequence was homologous to S-AKAP84, including a mitochondrial signal sequence near the amino terminus (Lin, R. Y., Moss, S. B., and Rubin, C. S. (1995) J. Biol. Chem. 270, 27804-27811). D-AKAP1 and the type I regulatory subunit appeared to have overlapping expression patterns in muscle and olfactory epithelium by in situ hybridization. These results raise a novel possibility that the type I regulatory subunit may be anchored via anchoring proteins.
Activity of Nitrogen-Containing and Non-Nitrogen-Containing Bisphosphonates on Tumor Cell Lines (2006)

We synthesized and tested three series of bisphosphonates for their activity in inhibiting the growth of three human tumor cell lines: MCF-7 (breast), NCI-H460 (lung), and SF-268 (CNS). The first series of compounds consisted of 49 nitrogen-containing bisphosphonates, the most active species being a tetrakispivaloyloxymethyl (POM) ester, having an (average) IC(50) of 6.8 microM. The second series of compounds consisted of nine terphenylbisphosphonates, the most active species also being a POM ester, having an IC(50) of 2.2 microM. The third series of compounds consisted of seven halogen or cyanophenylbisphosphonates, the most active species again being a POM ester, having an IC(50) of 500 nM. Taken together, these results are of interest because they show that bisphosphonate esters can have potent activity against a variety of tumor cell lines, with the most active terphenyl- and halophenyl-containing species having IC(50) values approximately 10-40x lower than the most potent commercially available bisphosphonates.