gebhart/patrepeval huggingface dataset:
Strong homophilic interactions of the Ig-like domains of polycystin-1, the protein product of an autosomal dominant polycystic kidney disease gene, PKD1 (2000)

The 14 kb mRNA of the polycystic kidney disease gene PKD1 encodes a novel large (approximately 460 kDa) protein, polycystin-1, of unknown function that is responsible for autosomal dominant polycystic kidney disease (ADPKD). The unique organization of multiple adhesive domains of polycystin-1, including 16 Ig-like domains (or PKD domains) suggests that it may play an important role in cell-cell/cell-matrix interactions. Here we demonstrate the localization of polycystin-1 to epithelial cell-cell contacts in culture. These results along with structural predictions prompted us to propose that polycystin-1 is involved in cell-cell adhesion through its cluster of Ig-like repeats. We show that Ig-like domains II-XVI are involved in strong calcium-independent homophilic interactions in vitro. Domains XI-XVI form interactions with high affinity (K(d) = 60 nM) and domains II-V exhibit the lowest binding affinity (K(d) = 730 nM) in these studies. Most importantly, we show that antibodies raised against Ig-like domains of polycystin-1 disrupt cell-cell interactions in MDCK cell monolayers, thus indicating that polycystin-1 is directly involved in the cell-cell adhesion process. Collectively, these data suggest that interactions of the Ig-like repeats of polycystin-1 play an important role in mediating intercellular adhesion. We suggest that the loss of these interactions due to mutations in polycystin-1 may be an important step in cystogenesis.
White-light-emitting CdSe quantum dots synthesized at room temperature (2006)

White-light-emitting CdSe quantum dots (QDs) were synthesized at room temperature (RT, ∼23°C) using an organometallic colloidal growth process. These QDs are characterized by high and reproducible quantum yields (ΦPL∼0.4) as well as by unusual spectral broadening [full width at half maximum (FWHM) ∼150nm) despite of their observed size monodispersity. Surface functionalization of these quantum dots using mercaptosuccinic acid made them soluble in water. A change of color together with an enhancement in ΦPL was observed upon surface functionalization.
Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols (2001)

The transferable potentials for phase equilibria-united atom (TraPPE-UA) force field for hydrocarbons is extended to primary, secondary, and tertiary alcohols by introducing the following (pseudo-)atoms: common hydroxyl O and H for all alcohols, α-CH3, α-CH2, α-CH, and α-C for methanol, primary, secondary, and tertiary alcohols, respectively. In the TraPPE-UA force field, the nonbonded interactions of these sites are governed by Lennard−Jones 12−6 potentials and Coulombic interactions of fixed partial charges. The values of these partial charges were borrowed from the optimized potentials for liquid simulations-united atom (OPLS−UA) force field [Jorgensen, W. L. J. Phys. Chem. 1986, 90, 1276]. The Lennard−Jones well depth and size parameters for the new interaction sites were determined by fitting to the single-component vapor−liquid-phase equilibria of a few selected model compounds. Although the well-depth parameters for the α-carbons could be taken directly from the TraPPE-UA parameters for the corresponding pseudoatoms in alkanes, the size parameters required small adjustments to reflect the differences in C−C and C−O bond lengths and the reduced electron density for α-carbons. Coupled−decoupled configurational-bias Monte Carlo simulations in the Gibbs and grand-canonical ensembles were carried out to calculate the one-component vapor−liquid coexistence curves for methanol, ethanol, propan-1-ol, propan-2-ol, butan-2-ol, 2-methylpropan-2-ol, pentan-1-ol, pentane-1,5-diol, and octan-1-ol, and to determine the binary phase diagrams for the mixtures of n-hexane/methanol and n-hexane/ethanol. It was found that the phase equilibria of the pure alcohols are accurately described by the TraPPE-UA force field, with mean unsigned deviations of about 1% from the experimental data for the normal boiling points and the saturated liquid densities. The azeotropic compositions for n-hexane/methanol and n-hexane/ethanol were predicted to be 0.340 at T = 448.15 K and 0.454 at 413.15 K and (in mole fraction of n-hexane), which are in good agreement with the experimental results of 0.288 and 0.440, respectively. Analysis of the structures of the n-hexane/methanol mixtures shows evidence for significant enhancements in the local mole fraction of alcohols in the vicinity of other alcohols. The magnitude of these local enhancements decreases with increasing alcohol concentration, but the change is gradual and no discontinuity was observed at the azeotropic composition.
Orthogonal matching pursuit for nonlinear unmixing of hyperspectral imagery (2014)

A simple but effective nonlinear mixture model is adopted for nonlinear unmixing of hyperspectral imagery, where the multiplication of each pair of endmembers results in a virtual endmember, representing multiple scattering effect during pixel construction process. The analysis is followed by linear unmixing for abundance estimation. Due to a large number of nonlinear terms being added in an unknown environment, the following abundance estimation may contain some error if most of endmembers do not really participate in the mixture of a pixel. Thus, sparse unmixing is applied to search the actual endmember set per pixel. The orthogonal matching pursuit (OMP) is adopted for this purpose. It can offer comparable results to the previously developed endmember variable linear mixture model (EVLMM) with much lower computational cost.
Mining motifs in massive time series databases (2003)

The problem of efficiently locating previously known patterns in a time series database (i.e., query by content) has received much attention and may now largely be regarded as a solved problem. However, from a knowledge discovery viewpoint, a more interesting problem is the enumeration of previously unknown, frequently occurring patterns. We call such patterns "motifs", because of their close analogy to their discrete counterparts in computation biology. An efficient motif discovery algorithm for time series would be useful as a tool for summarizing and visualizing massive time series databases. In addition it could be used as a subroutine in various other data mining tasks, including the discovery of association rules, clustering and classification. In this paper we carefully motivate, then introduce, a nontrivial definition of time series motifs. We propose an efficient algorithm to discover them, and we demonstrate the utility and efficiency of our approach on several real world datasets.
Noncytolytic extraction of murine tumor-specific transplantation antigens with the nonionic detergent octyl-beta-D-glucopyranoside. (1982)

The nonionic detergent octyl-beta-D-glucopyranoside (C8Glu) was used to extract immunogenic tumor-specific transplantation antigen (TSTA) from intact cells and purified plasma membranes of the 3-methylcholanthrene-induced fibrosarcoma MCA-F. Pretreatment of syngeneic C3H/HeJ mice with 100 micrograms of C8Glu extracts induced specific immunoprotection such that mice resisted the outgrowth of MCA-F but not the antigenically distinct tumors MCA-D or MCA-2A. Incubation of intact cells with 7 mM (0.2%) C8Glu for 30 minutes at 23 degrees C was judged to be noncytolytic because extracted cells excluded trypan blue. Preparative isoelectric focusing partially purified the MCA-F-specific antigen from crude C8Glu extracts into the pH 6.5-6.8 region of the gradient. Electrofocusing yielded 60% of the applied antigen activity and a fourfold to fivefold increase in specific activity. In addition, immunoprotective activity was obtained in 2% C8Glu extracts of MCA-F plasma membranes, confirming the membrane localization of the MCA-FTSTA. Three properties of C8Glu rendered it an attractive agent for the preparation of cell surface proteins: a nonionic character, large critical micellar concentration, and its capacity to extract antigens without complete membrane solubilization or cell disruption.
Distributed dynamic channel assignment schemes (2002)

Some distributed channel schemes for a one-dimensional cellular radio system are described. The channel assignment in the schemes proposed is based on signal strength measurements and therefore gives an improvement in capacity over schemes using reuse distance criterion for channel assignment. The proposed schemes are evaluated by simulations and their behavior with variation in traffic density, size of the channel set and number of reassignments is studied.
Quantitative trait loci influencing cholesterol and phospholipid phenotypes map to chromosomes that contain genes regulating blood pressure in the spontaneously hypertensive rat. (1996)

The frequent coincidence of hypertension and dyslipidemia suggests that related genetic factors might underlie these common risk factors for cardiovascular disease. To investigate whether quantitative trait loci (QTLs) regulating lipid levels map to chromosomes known to contain genes regulating blood pressure, we used a genome scanning approach to map QTLs influencing cholesterol and phospholipid phenotypes in a large set of recombinant inbred strains and in congenic strains derived from the spontaneously hypertensive rat and normotensive Brown-Norway (BN.Lx) rat fed normal and high cholesterol diets. QTLs regulating lipid phenotypes were mapped by scanning the genome with 534 genetic markers. A significant relationship (P < 0.00006) was found between basal HDL2 cholesterol levels and the D19Mit2 marker on chromosome 19. Analysis of congenic strains of spontaneously hypertensive rat indicated that QTLs regulating postdietary lipid phenotypes exist also on chromosomes 8 and 20. Previous studies in the recombinant inbred and congenic strains have demonstrated the presence of blood pressure regulatory genes in corresponding segments of chromosomes 8, 19, and 20. These findings provide support for the hypothesis that blood pressure and certain lipid subfractions can be modulated by linked genes or perhaps even the same genes.
Stochastic Response of Hysteretic Systems to Narrow-Band Excitation (1994)

Technical Briefs Stochastic Response of Hysteretic Systems to Narrow-Band Excitation W. Q. Zhu, W. Q. Zhu Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 Search for other works by this author on: This Site PubMed Google Scholar C. D. Huang, C. D. Huang Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 Search for other works by this author on: This Site PubMed Google Scholar T. T. Soong T. T. Soong Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information W. Q. Zhu Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 C. D. Huang Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 T. T. Soong Department of Civil Engineering, State University of New York at Buffalo, Buffalo, NY 14260 J. Appl. Mech. Mar 1994, 61(1): 211-213 (3 pages) https://doi.org/10.1115/1.2901405 Published Online: March 1, 1994 Article history Received: May 27, 1992 Revised: November 23, 1992 Online: March 31, 2008
Improperly placed anterior cruciate ligament grafts: correlation between radiological parameters and clinical results (2000)

Despite increasing knowledge on knee biomechanics and refined operative techniques, an increasing number of patients are being seen with failed anterior cruciate ligament (ACL) reconstruction. Failure of the reconstruction and further damage to the knee are correlated with improper placement of the graft, which interferes with graft biology and biomechanical demands. Between 1994 and 1995, 63 patients with improperly placed ACL grafts were referred to our institution because of persistent knee instability and pain. A method for analysis of the femoral drill hole on radiography was developed. Before reoperation the radiograph was evaluated by our method, noting the clinical aspects according to the recommendations of the International Knee Documentation Committee (IKDC). The femoral placement of the ACL graft could easily be defined on the lateral and anteroposterior tunnel radiography. The most common error was a femoral placement anterior to the anatomical insertion of the ACL. A significant correlation (P < 0.05) was found between femoral placement of the graft in the sagittal plane and clinical results: the IKDC score declined with increasing distance of the graft from the most isometric bundle of the ACL in the anteroposterior direction.
Low-loss Ti:LiNbO&lt;inf&gt;3&lt;/inf&gt;waveguide bends at λ = 1.3 µm (1982)

Low-loss waveguide bends are necessary for many proposed integrated optical circuits. The bend loss associated with an <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</tex> -shaped transition connecting offset 6 μm wide titanium-indiffused lithium niobate strip waveguides has been measured as a function of transition length and initial Ti metal thickness for 1.3 μm wavelength. Losses as low as 0.2 ± 0.2 dB have been achieved for a transition between offset parallel waveguides with a 0.1 mm lateral and 3.25 mm longitudinal separation. The bend loss is shown to be strongly dependent on the mode confinement and less sensitive to the shape of the transition curve.
Conventional Technological Boosters for Injection Velocity in Ultrathin-Body MOSFETs (2007)

To meet ITRS requirements, highly scaled MOSFETs will have to operate close to the quasi-ballistic regime and to exhibit enhanced injection velocity. Good performances may be achieved thanks to high transport materials such as germanium or III-V semiconductors. However their integration is still very challenging. Following a different approach, this paper proposes to examine how to improve the injection in conventional (100) silicon ultrathin-body (UTB) MOSFETs. A systematic investigation of the impact of the different usual technological parameters highlights that SG and DG exhibit comparable performances and that no improvement in the injection velocity is expected with the silicon thickness thinning down to 4 nm. Moreover the degradation of the injection velocity with the integration of high- dielectrics is shown. Finally, a significant improvement of the injection velocity due to a higher confinement in asymmetrical double gate MOSFET has been found. Similarly, it is shown that, single gate UTB MOSFETs with thin buried oxide (BOX) exhibit an enhanced injection velocity. In conclusion, only the reduction of the BOX thickness and the integration of strained channel have been found to be realistic and significant boosters of the injection velocity in silicon (100) MOSFETs. Prediction of the evolution of the injection velocity along the roadmap, using a pragmatic strategy of scaling, confirms that these two parameters will play a significant role in improving highly scaled (100) silicon devices performances.
Real-time analysis of the transcriptional regulation of hiv and hcmv promoters in single mammalian cells (1995)

The regulation of human cytomegalovirus (hCMV) and human immunodeficiency virus (HIV) gene expression has been studied in single intact mammalian cells. Viral promoters were placed upstream of the firefly luciferase reporter gene and the resulting hybrid reporter constructs were stably integrated into the HeLa cell genome. A highly sensitive photon-counting camera system was used to study the level of gene expression in single intact cells. Luciferase expression was studied in the absence of activators of viral gene expression, in the presence of the HIV-1 TAT transactivator protein, or in the presence of sodium butyrate, a non-viral activator of gene expression. In the absence of any activator of gene expression, while expression was undetectable in most cells, significant levels of basal luciferase activity were observed in a few cells, indicating heterogeneity in gene expression in the cell population. In the presence of the general activator of viral gene expression, sodium butyrate, transcriptional activation from the viral promoters gave rise to significant and relatively homogeneous levels of luciferase expression in a majority of cells. The luciferase imaging technology was used for the real-time analysis of changes of gene expression within a single cell. This non-invasive reporter assay should become important for studies of the temporal regulation of gene expression in single cells.
Block Interleaved Frequency Division Multiple Access for Power Efficiency, Robustness, Flexibility, and Scalability (2009)

The multiple access solution in an IMT-Advanced mobile radio system has to meet challenging requirements such as high throughput, low delays, high flexibility, good robustness, low computational complexity, and a high power efficiency, especially in the uplink. In this paper, a novel multiple access scheme for uplinks denoted as B-IFDMA is presented. We show that this scheme is able to provide equal or better error rate performance than the Single-Carrier Frequency Division Multiple Access (SCFDMA) schemes IFDMA and LFDMA, when considering realistic channel estimation performance at the receiver and no reliable channel state information at the transmitter. We also show that B-IFDMA provides better amplifier efficiency than OFDMA and can provide better end-to-end energy efficiency than IFDMA and LFDMA. Moreover, the scheme shows a promisingly high robustness to frequency-offsets and Doppler spread. Thus, this scheme can be regarded as a promising solution for the uplink of future mobile radio systems.
Prediction of Drug Dissolution from Tablets Using Near‐Infrared Diffuse Reflectance Spectroscopy as a Nondestructive Method (2004)

The goal of this study is to use near-infrared (NIR) reflectance spectroscopy to measure the percentage drug dissolution from a series of tablets compacted at different compressional forces, calibrate NIR data vs. laboratory equipment data, develop a model equation, validate the model, and test the model predictive ability. Seven theophylline tablet formulations of the same composition but with different dissolution profiles were prepared. Laboratory dissolution profiles were compared with NIR diffuse reflectance data. Linear regression, quadratic, cubic, and partial least-square techniques were used to determine the relationship between dissolution profiles data and NIR spectra. The results demonstrated that a decrease in the amount of drug dissolution produced an increase in NIR absorbance. A series of model equations, depending on the mathematical technique used for regression, were developed from the calibration of the percentage of drug dissolution by using laboratory equipment vs. the NIR diffuse reflectance for each formulation. The results of NIR dissolution data were similar to laboratory tests. The NIR diffuse reflectance spectroscopy method is an alternative, nondestructive method for measurement of drug dissolution from tablets.
Role for the Target Enzyme in Deactivation of Photoreceptor G Protein in Vivo (1998)

Heterotrimeric guanosine 5'-triphosphate (GTP)-binding proteins (G proteins) are deactivated by hydrolysis of the GTP that they bind when activated by transmembrane receptors. Transducin, the G protein that relays visual excitation from rhodopsin to the cyclic guanosine 3',5'-monophosphate phosphodiesterase (PDE) in retinal photoreceptors, must be deactivated for the light response to recover. A point mutation in the gamma subunit of PDE impaired transducin-PDE interactions and slowed the recovery rate of the flash response in transgenic mouse rods. These results indicate that the normal deactivation of transducin in vivo requires the G protein to interact with its target enzyme.
Treatment options for early Parkinson's disease. (1996)

Proper treatment of tremor in any clinical setting depends on correct diagnosis. Essential, or familial, tremor is symptomatic with movement and involves the limbs, head and voice. Parkinson's disease tremor occurs at rest, involves the jaw and limbs and is associated with bradykinesia, rigidity and falling. Parkinson's disease is treated with a number of medications, but levodopa, a dopamine precursor, is considered most effective. Other therapies in the early stages of Parkinson's disease may include neuroprotective agents, dopamine agonists, dopamine reuptake inhibitors, anticholinergics and/or amantadine. Polypharmacy is often necessary to minimize or avoid drug side effects.
Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes   (2014)

Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.