gebhart/patrepeval huggingface dataset:
Size matters: Molecular weight affects the efficiency of poly(ethylenimine) as a gene delivery vehicle (1999)

Poly(ethylenimine) (PEI) samples of various molecular weights and pHs were used to transfect endothelial cells to achieve levels of gene expression for comparison. PEIs with nominal molecular weights of 600, 1200, 1800, 10,000, and 70,000 Da were examined at pHs of 5. 0, 6.0, 7.0, and 8.0, and the results were recorded in terms of transfection efficiencies at 24, 48, 68, 92, and 120 h post-transfection. Trials were performed on the human endothelial cell-derived cell line EA.hy 926. We found that, for the polymers tested, transfection efficiency increased as the molecular weight of PEI increased. Representative values of PEIs at pH 6 and molecular weight 70,000 produced average transfection efficiencies of 25.6 +/- 7.9% (n = 8) at the greatest average expression levels, while PEI of molecular weight 10,000 yielded efficiencies of only 11.4 +/- 1.7% (n = 6). Transfection efficiencies for molecular weight 1,800 PEI were essentially zero, and PEIs of lower molecular weights produced no transfection at all. In contrast, the pH of the PEI solutions had no discernible effect on transfection. Optimal expression of the green fluorescent protein reporter occurred between 2 and 3 days post-transfection. The amount of reporter expression also was noted, as determined by the brightness of fluorescing cells under UV. The data obtained demonstrate that the molecular weight of the PEI carrier has an effect on transfection efficiency while the pH of the PEI solutions prior to DNA complexation has no such effect.
A new center-biased search algorithm for block motion estimation (2002)

Experimental results show that the block motion field of a real world image sequence is usually gentle, smooth, and varies slowly, as a result in a center-biased global minimum motion vector distribution instead of an uniform distribution. Based on this characteristic of the image sequence a new four-step search (4SS) algorithm with a center-biased checking point pattern for fast block motion estimation is proposed. A variable searching-step technique is employed in the proposed algorithm with a minimum of 2 searching steps and a maximum of 4. The total number of checking points is varied from 17 to 27. Simulation results show that, as compared to the well-known three-step search, the proposed 4SS produces smaller motion compensation errors with a smaller computational requirement. The 4SS also possesses hardware-oriented features regularity and simplicity.
Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs (2012)

In human mitochondria, 1-methyladenosine (m¹A) occurs at position 58 of tRNA(Leu(UUR)). In addition, partial m¹A58 modifications have been found in human mitochondrial tRNA(Lys) and tRNA(Ser(UCN)). We identified human Trmt61B, which encodes a mitochondria-specific tRNA methyltransferase responsible for m¹A58 in these three tRNAs. Trmt61B is dominantly localized to the mitochondria. m¹A58 formation in human mitochondrial tRNA(Leu(UUR)) could be reconstituted in vitro using recombinant Trmt61B in the presence of Ado-Met as a methyl donor. Unlike the cytoplasmic tRNA m¹A58 methyltransferase that consists of an α2β2 heterotetramer formed by Trmt61A and Trmt6, Trmt61B formed a homo-oligomer (presumably a homotetramer) that resembled the bacterial homotetrameric m¹A58 methyltransferase. The bacterial origin of Trmt61B is supported by the results of the phylogenetic analysis.
Neural network control for DC motor micromaneuvering (1995)

The application of a neural network controller for compensating the effects induced by the friction in a DC motor micromaneuvering system is considered in this article. A backpropagation neural network operating in the specialized learning mode, using the sign gradient descent algorithm, is employed. The input vector to the neural network controller consists of the time history of the motor angular shaft velocity within a prespecified time window. The on-line training of the neural network is performed in the region of interest of the output domain. The neural network output resembles that of a pulse width modulated controller. The effect of the number of neurons in the input and hidden layers on the transient system response is explored. Experimental studies are presented to indicate the effectiveness of the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The bromodomain interaction module (2012)

ε-N-acetylation of lysine residues (K(ac)) is one of the most abundant post-translation modifications (PTMs) in the human proteome. In the nucleus, acetylation of histones has been linked to transcriptional activation of genes but the functional consequences of most acetylation events and proteins recruited to these sites remains largely unknown. Bromodomains (BRDs) are small helical interaction modules that specifically recognize acetylation sites in proteins. BRDs have recently emerged as interesting targets for the development of specific protein interaction inhibitors, enabling a novel exiting strategy for the development of new therapies. This review provides an overview over sequence requirements of BRDs, known substrates and the structural mechanisms of specific K(ac) recognition.
S100β as a biomarker for differential diagnosis of intracerebral hemorrhage and ischemic stroke (2016)

S100β could serve as a potential biomarker for differentiating between ICH and IS and predicting short-term functional outcome after ICH.
Environmental effects on the streaming mode performance of metal evaporated and metal particle tapes (1997)

A commercial Hi-8 video cassette recorder was instrumented to measure friction force between the rotary heads and tape, rms head output, and signal dropouts to sub /spl mu/s duration. Streaming (play) mode experiments using metal evaporated (ME) and metal particle (MP) tapes were performed at design tension under equilibrium and nonequilibrium conditions inside of an environmental chamber at various temperature and specific humidity (SH=ratio of the weights of water vapor to dry air in the mixture). Interface stability and recording performance at a 0.6 /spl mu/m recording wavelength were measured to bit level resolution using a dropout counter and changes in rms head output were correlated to changes in head-to-tape spacing using the Wallace equation. ME tape performed best at moderate SH (from 0.009 to 0.013) in the operating temperature range of 15.6 to 32.2/spl deg/C, whereas MP tape performed best at low temperature. At a given temperature, higher SH increased normal and friction forces and decreased head-to-tape spacing due to spontaneous water meniscus formation between contacting and noncontacting asperities on the head, tape, and debris particle surfaces. Dropout frequency and interface stability were sensitive to both SH and temperature. Humidity dependence was governed by the relative size difference between wear debris particles and spontaneously formed water menisci. Competing mechanisms of increased lubricant mobility and spontaneously formed water menisci of smaller radii of curvature at higher temperature governed temperature dependence. A model based on capillary condensation of water vapor onto surfaces in a sliding contact is developed to explain experimental data. An expression for meniscus force consisting of both Laplace and surface tension contributions is developed for nanometer size contact spots and wear debris particles. The model predicts that meniscus force will increase and head-to-tape spacing will decrease with increasing SH which was observed experimentally. Four lubrication regimes are defined for wear debris particles passing through the contact interface. Both SH and extent of deformation of a particle determine whether menisci will form around the particle, and presence or absence of associated meniscus forces explains trends in dropout frequency data. The model allows determination of meniscus height from which minimum values of Kelvin radius and relative humidity (RH) in the contact interface can be calculated. Proximity and intimate contact of the surfaces increases RH and SH in the contact interface over that maintained in the environmental chamber to near their saturation values.
Reading behavior predicts syntactic categories (2015)

It is well-known that readers are less likely to fixate their gaze on closed class syntactic categories such as prepositions and pronouns.This paper investigates to what extent the syntactic category of a word in context can be predicted from gaze features obtained using eye-tracking equipment.If syntax can be reliably predicted from eye movements of readers, it can speed up linguistic annotation substantially, since reading is considerably faster than doing linguistic annotation by hand.Our results show that gaze features do discriminate between most pairs of syntactic categories, and we show how we can use this to annotate words with part of speech across domains, when tag dictionaries enable us to narrow down the set of potential categories.
Distribution of β3-adrenoceptor mRNA in human tissues (1995)

The beta 3-adrenoceptor is a G protein-coupled receptor which mediates metabolic functions of the endogenous catecholamines epinephrine and norepinephrine. Questions exist regarding distribution of the beta 3-adrenoceptor in human tissue. In order to examine the distribution of beta 3-adrenoceptor mRNA in human tissues, we used sensitive and specific RNase protection assays without previous PCR amplification in an extensive list of human tissues. We confirm the presence of beta 3-adrenoceptor mRNA in human white fat from several locations, gall bladder, and small intestine, as well as extend the distribution of beta 3-adrenoceptor mRNA to previously uncharacterized human tissues such as stomach and prostate. The presence of beta 3-adrenoceptor mRNA in human white adipose tissue has important implications regarding possible use of beta 3-adrenoceptor selective agonists as anti-obesity agents, and the demonstration of beta 3-adrenoceptor mRNA in a number of gastrointestinal tissues and prostate raises the question of the role of the beta 3-adrenoceptor in motility and secretory processes.
Antimalarial activities of oligodeoxynucleotide phosphorothioates in chloroquine-resistant Plasmodium falciparum. (1992)

Synthetic oligonucleotides and their chemical modifications have been shown to inhibit viral and cellular gene expression by sequence-specific antisense hybridization to target mRNAs. We now report that oligodeoxynucleotide phosphorothioates and their nuclease-resistant modifications are effective in micromolar and submicromolar concentrations against the growth of both chloroquine-resistant and chloroquine-sensitive strains of Plasmodium falciparum in vitro. Parasitized human erythrocytes were found to be accessible to radioactively labeled oligodeoxynucleotides, whereas the uninfected erythrocytes did not permit any cellular entry of the same compounds. The dihydrofolate reductase-thymidylate synthase gene of P. falciparum was demonstrated to be a good target for sequence-dependent inhibition of plasmodial growth by exogenously administered modified oligonucleotides. The antimalarial activities observed in vitro were identical for chloroquine-sensitive and chloroquine-resistant strains of P. falciparum. The antimalarial activity of oligodeoxynucleotide phosphorothioates is related to sequence complementarity to certain regions of the plasmodial genome as well as to non-sequence-defined activities.
Development of Novel Quinone Phosphorodiamidate Prodrugs Targeted to DT-Diaphorase (2000)

A series of naphthoquinone and benzimidazolequinone phosphorodiamidates has been synthesized and studied as potential cytotoxic prodrugs activated by DT-diaphorase. Reduction of the quinone moiety in the target compounds was expected to provide a pathway for expulsion of the phosphoramide mustard alkylating agent. All of the compounds synthesized were excellent substrates for purified human DT-diaphorase (k(cat)/K(m) = 3 x 10(7) - 3 x 10(8) M(-1) s(-1)). The naphthoquinones were toxic to both HT-29 and BE human colon cancer cell lines in a clonogenic assay; however, cytotoxicity did not correlate with DT-diaphorase activity in these cell lines. The benzimidazolequinone analogues were 1-2 orders of magnitude less cytotoxic than the naphthoquinone analogues. Chemical reduction of the naphthoquinone led to rapid expulsion of the phosphorodiamidate anion; in contrast, the benzimidazole reduction product was stable. Michael addition of glutathione and other sulfur nucleophiles provides an alternate mechanism for activation of the naphthoquinone phosphorodiamidates, and this mechanism may contribute to the cytotoxicity of these compounds.
Oxidation of Human Insulin-Like Growth Factor I in Formulation Studies. 3. Factorial Experiments of the Effects of Ferric Ions, EDTA, and Visible Light on Methionine Oxidation and Covalent Aggregation in Aqueous Solution (1997)

The influence of ferric ions, EDTA, and visible light on the oxidation of methionine and the covalent reducible and nonreducible dimerization in human Insulin-like Growth Factor I (hIGF-I) in aqueous (1 mM) phosphate buffer solution were studied. A reduced factorial experiment with two levels of each factor was used. Regression models for the three responses were constructed with partial least square (PLS) analysis. The hIGF-I variants were quantified by reversed-phase high-performance liquid chromatography (RP-HPLC), gel filtration, and reduced sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The formation of the hIGF-I variants in aqueous solution at pH 6.1 exhibited different dependencies on the variables studied. The oxidation of methionine was affected mainly by visible light and the combination of 10 ppm ferric ions and 20 ppm EDTA, whereas ferric ions alone had no significant effect. The covalent dimerization of hIGF-I was correlated to visible light and ferric ions. The interaction effects of ferric ions with either visible light or EDTA were also significant on the dimerization rates. Both reducible and nonreducible soluble covalent dimers were formed, with the reducible dimer being the most prominent. The oxidation of methionine 59 in hIGF-I is catalyzed by light and by ferric ions in combination with EDTA. The covalent dimerization of hIGF-I is mainly affected by light and by ferric ions. Both reducible and nonreducible dimerization increased by oxidative conditions. Human IGF-I appears to dimerize covalently by both disulfide scrambling and by a radical-promoted nondisulfide pathway. EDTA is necessary for ferric ions to be active in the oxidation of methionine in hIGF-I but not for the covalent dimerization.
Duplication of the tuf gene, which encodes peptide chain elongation factor Tu, is widespread in Gram-negative bacteria (1981)

The tuf gene which encodes peptide chain elongation factor Tu was found to be duplicated in nine enteric and four nonenteric gram-negative bacteria, but present only in one copy in two gram-positive genera. In two of the nonenteric gram-negative genera, Pseudomonas and Caulobacter, the duplicate tuf genes were found to be very close together on the chromosome, which contrasts with the situation in Escherichia coli, where they are more than 660 kilobases apart.
Phagocytic Rabbit Cell Lines Expressing Class II MHC Products: Establishment of Cell Lines by Viral Transformation (1986)

Continuous rabbit macrophage-like cell lines were established after in vitro infection of spleen cells with either Simian virus 40, lymphotropic papovavirus or herpesvirus sylvilagus. These cell lines are characterized as morphologically similar to mature macrophages, esterase positive, and have unrearranged immunoglobulin genes. They possess macrophage functionality because they are highly phagocytic and are able to mediate an antibody dependent cell mediated cytotoxicity assay on chicken red blood cells. Northern blot analysis of total cellular RNA with a DQ alpha probe indicates that the cell lines constitutively express message for class II gene products. In addition, cell sorter analysis indicates that two of these lines display class II antigen at the cell surface.
Aurin tricarboxylic acid: a novel inhibitor of the association of von Willebrand factor and platelets (1988)

Shear stress activated platelets undergo aggregation in the presence of large or unusually large von Willebrand factor (vWF) multimers without the addition of ristocetin or any other exogenous chemical. This phenomenon may be analogous to the platelet aggregation that leads to thrombosis in the narrowed arteries and arterioles of patients with atherosclerosis or vasospasm. A triphenyl-methyl compound, aurin tricarboxylic acid (ATA), inhibits shear-induced, vWF-mediated platelet aggregation in platelet-rich plasma (PRP) in concentrations above 200 mumol/L and in buffer suspensions of washed platelets at a concentration of 0.1 mumol/L. In a concentration-dependent manner, ATA also inhibits ristocetin-induced, vWF-mediated platelet clumping in both fresh and formaldehyde-fixed platelet suspensions. This inhibition can be overcome by increasing the concentration of vWF, following the kinetics of first order competitive inhibition. ATA prevents the attachment to platelets of the largest vWF multimeric forms found in normal plasma and of the unusually large vWF multimers derived from endothelial cells. The rate of aggregation and degree of inhibition by ATA is not accounted for by the binding of ristocetin or calcium. Arachidonic acid- and adenosine diphosphate (ADP)-induced aggregation are not inhibited by ATA. Platelets incubated with ATA can be easily separated from the compound. However, ATA binds to large vWF multimeric forms and inhibits their ristocetin-induced interaction with platelet glycoprotein Ib. Because ATA also inhibits shear-induced, vWF-mediated platelet aggregation in vitro in the absence of ristocetin, it may be a useful prototype compound to impede the development of arterial thrombosis in vivo.
Stereoselective inhibition of human platelet aggregation by R-138727, the active metabolite of CS-747 (Prasugrel, LY640315), a novel P2Y12 receptor inhibitor (2005)

Summary CS-747 (Prasugrel, LY640315) is a thienopyridine antiplatelet prodrug that is metabolized to the thiol-containing active metabolite R-138727, which binds to and irreversibly inhibits the platelet P2Y12 ADP receptor. R-138727 is composed of 4 stereoisomers, (R, S)-, (R, R)-, (S, S)-, and (S, R)-isomers (the first letter for the configuration of a chiral center at the sulfur-bearing position and the second for that at the benzylic position). In the present study, we determined the stereoselectivity of P2Y12 antagonist effects by assessing the antagonism of the [3H]-2-MeS-ADP that binds to human P2Y12 receptors expressed in Chinese hamster ovary cells as an affinity assay, and by the inhibition of ADP-induced aggregation of washed human platelets as a functional assay. R-138727 and its 2 components, R-99224, a mixture of (R, S)- and (S, R)-isomers and R-100364, a mixture of (R, R)- and (S, S)-isomers, inhibited [3H]-2-MeS-ADP binding and platelet aggregation. The rank order of potency of these compounds were identical in both assays: R-99224&gt;R-138727&gt;&gt; R-100364. Inhibition of ADP-induced platelet aggregation by R-138727 and R-99224 was concentration- and time-related. In experiments using the 4 single stereo-isomers, all isomers inhibited ADP-induced platelet aggregation, but the (R, S)-isomer was found to be the most potent, followed by the (R, R)-isomer. These in vitro studies indicate that R-138727 is an effective antagonist of P2Y12 and potent inhibitor of ADP-induced platelet aggregation, and that these antiplatelet activities of R-138727 are largely dependent on its (R, S)-isomer. This suggests that the (R)- configuration of the reactive thiol group of the active metabolite of CS-747 is critical for P2Y12 and platelet inhibitory activities.
Quantitative studies of spin-momentum-transfer-induced excitations in Co/Cu multilayer films using point-contact spectroscopy (2003)

We have measured current-induced magnetic excitations in a variety of exchange-coupled Co/Cu multilayers using point-contact spectroscopy. A step in the dc resistance and corresponding peak in dV/dI are observed at a critical current Ic whose value depends linearly on applied magnetic field Bapp′ in agreement with Slonczewski’s theory. These features are observed for both in- and out-of-plane fields. Excitations in ferromagnetically coupled films occur even without an applied field. The spin transfer efficiency is determined from the slope and intercept of Ic vs Bapp and varied from contact to contact. For out of plane magnetized samples, the deduced spin transfer efficiency values are in good agreement with the predictions of Slonczewski.
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation (2012)

DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.
Coherent population dynamics of a three-level atom in spacetime (2002)

This work explores temporal and spatial aspects of coherent population transfer in a three-level atom through a synergic combination of experimental measurements and theoretical calculations. Experimental measurements exploit the broad bandwidth of a femtosecond laser pulse to initiate simultaneous excitation of the $5p{}^{2}{P}_{1/2}\ensuremath{\leftarrow}5s{}^{2}{S}_{1/2}$ and $5p{}^{2}{P}_{3/2}\ensuremath{\leftarrow}5s{}^{2}{S}_{1/2}$ components of the doublet line of atomic rubidium. By adjusting positive or negative frequency sweeps the pump pulse favors either one of the two transitions and eventually even decouples the two excited states. The population of the excited spin-orbit levels is monitored in real time by stimulated emission probing under conditions of different intensity, chirp, and pulse width of the driving field, giving detailed information on the coupling between the three levels and their interactions with the driving and probe fields at different points in spacetime. Both pump and probe pulses are carefully characterized after the interaction region by frequency-resolved optical gating. In order to interpret and understand the experimental results it is essential to consider the close relationship between pulse propagation and time evolution of the atomic system via the coupled Maxwell-Bloch equations. This analysis highlights the importance of spatial propagation of the light fields, as well as their temporal dependence, in understanding the dynamical population evolution, and quantitatively reproduces all aspects of the experimental measurements.
Cisplatin Plus Gemcitabine Versus a Cisplatin-Based Triplet Versus Nonplatinum Sequential Doublets in Advanced Non–Small-Cell Lung Cancer: A Spanish Lung Cancer Group Phase III Randomized Trial (2003)

On the basis of these results, CG remains a standard regimen for first-line treatment of advanced NSCLC.