gebhart/patrepeval huggingface dataset:
The palmitoylated cysteine of the cytoplasmic tail of alpha 2A-adrenergic receptors confers subtype-specific agonist-promoted downregulation. (1994)

Most guanine nucleotide binding protein (G protein)-coupled receptors have a conserved cysteine in the C-terminal cytoplasmic tail near the seventh transmembrane spanning region. This cysteine is known to be palmitoylated in rhodopsin, the beta 2-adrenergic receptor (beta 2AR) and the alpha 2A-adrenergic receptor (alpha 2AAR). For the beta 2AR, this cysteine has been shown to be important for stimulatory G protein (Gs) coupling and agonist-promoted desensitization. For the alpha 2AAR (human alpha 2 C10) palmitoylation occurs at Cys-442, but it is not known what function such fatty acid acylation subserves. The closely related alpha 2CAR subtype denoted alpha 2C4 lacks a cysteine in this region and has different G-protein-coupling characteristics and agonist regulatory properties as compared to alpha 2C10. To assess the role of the palmitoylcysteine in alpha 2AR function, we constructed a mutated alpha 2C10 having a phenylalanine (the analogous amino acid in the alpha 2C4 in this position) substituted for Cys-442, denoted alpha 2C10(Phe-442), and expressed this along with wild-type alpha 2C10 and alpha 2C4 in CHO cells. Functional coupling to inhibitory G protein (Gi) and to Gs was identical between wild-type alpha 2C10 and alpha 2C10(Phe-442). Agonist-promoted desensitization of both the Gi and Gs-mediated pathways was also found to be unaffected by this mutation. Cellular trafficking induced by agonist exposure was evaluated by delineation of intracellular (sequestered) versus cell surface receptors and by determination of net receptor loss. Mutation of Cys-442 did not alter the extent or rate of agonist-promoted sequestration induced by agonists or the recovery from sequestration. However, the downregulation of receptor number after prolonged agonist exposure was completely abolished by this mutation and converted alpha 2C10 to an alpha 2C4 phenotype in regard to this adaptive response. Another mutated alpha 2C10, in which Cys-442 was replaced by alanine, also failed to downregulate. Thus, the function of this cytoplasmic palmitoylcysteine is distinctly different between the alpha 2AR and other G-protein-coupled receptors such as the beta 2AR and rhodopsin, and this suggests that this molecular attribute may subserve diverse roles among members of this family of receptors. For the alpha 2ARs, this may represent an evolved feature that provides for differing needs for regulation of the alpha 2C10 and alpha 2C4 subtypes by agonist.
β‐Amyrin synthase (1998)

Beta-amyrin, a typical pentacyclic triterpene having an oleanane skeleton, is one of the most commonly occuring triterpenes in nature and is biosynthesized from (3S)-2,3-oxidosqualene. The enzyme, beta-amyrin synthase, catalyzing the cyclization of oxidosqualene into beta-amyrin, generates five rings and eight asymmetric centers in a single transformation. A homology-based PCR method was attempted to obtain the cDNA of this enzyme from the hairy root of Panax ginseng which produces oleanane saponins together with dammarane-type saponins. Two sets of degenerate oligonucleotide primers were designed at the regions which are highly conserved among known oxidosqualene cyclases (OSCs). Nested PCRs using these primers successfully amplified the core fragment which revealed the presence of two OSC clones PNX and PNY. Specific amplification of each clone by 3'-RACE and 5'-RACE was carried out to obtain the whole sequences. The two clones exhibited 60% amino acid identity to each other. A full-length clone of PNY was ligated into the yeast expression vector pYES2 under the GAL1 promoter to give pOSC(PNY). Beta-amyrin production was observed with the mutant yeast lacking lanosterol synthase, transformed by this plasmid. The sequence of pOSC(PNY) contains an open reading frame of 2289 nucleotides which codes for 763 amino acids with a predicted molecular mass of 88 kDa. Sequence comparison with other OSCs showed a high level of similarity with lanosterol, cycloartenol and lupeol synthases. The other clone, pOSC(PNX), was shown to be cycloartenol synthase by similar expression in yeast. The present studies have revealed that distinct OSC exists for triterpene formation in higher plants, and the high level of similarity with cycloartenol synthase indicates close evolutional relationship between sterol and triterpene biosynthesis.
A 3D human teeth database construction based on a point-based shape registration (2011)

We propose a new system for building a 3D database for human teeth. Real extracted human teeth are scanned using a cone-beam CT scanner to build. The teeth models are segmented from the resulting images by means of level sets. The database includes 3D models of these teeth after minimizing global differences between the models. An affine transformation function is used to model the differences between the models. The transformation parameters are estimated by minimizing a least squares energy. A total of 280 teeth 3-D models have been created to build the real database and demonstrate the performance of the proposed framework.
The Conserved Seven-Transmembrane Sequence NP(X)2,3Y of the G-Protein-Coupled Receptor Superfamily Regulates Multiple Properties of the .beta.2-Adrenergic Receptor (1995)

The beta 2-adrenergic receptor (beta 2AR) is a member of a large superfamily of seven transmembrane domain, G-protein-coupled receptors. Within the putative seventh transmembrane domain of the beta 2AR is a sequence of amino acids, NPLIY, which is conserved with minor variations in all members of the superfamily. Previously it was demonstrated that mutation of tyrosine residue 326 to an alanine abolished agonist promoted sequestration of this mutant without affecting its ability to maximally stimulate adenylyl cyclase in membranes [Barak, L.S., Tiberi, M., Freedman, N.J., Kwatra, M.M., Lefkowitz, R.J., & Caron M.J. (1994) J Biol. Chem. 269, 2790-2795]. In the present study we characterized the NPLIY amino acid sequence in an attempt to determine how it can affect the agonist-mediated sequestration of the beta 2AR and to test whether it is a functional motif. We find that point mutations of the most conserved amino acids, N, P, and Y, in this sequence affect several other receptor properties in addition to sequestration. Mutation of asparagine 322 to an alanine resulted in complete uncoupling of the receptor, loss of high-affinity agonist binding, and abolition of receptor sequestration, down-regulation, and phosphorylation. In contrast, a conservative mutation of this residue to an aspartic acid (as found in the thrombin receptor) resulted in an improvement of G-protein coupling without adversely affecting other receptor properties. Substitution of proline residue 323 with an alanine residue resulted in a receptor with mild deficits in sequestration and coupling, a reduced agonist-mediated phosphorylation, and no change in down-regulation.(ABSTRACT TRUNCATED AT 250 WORDS)
A Comparative Analysis on the Living Culture of Undergraduate Students for Establishment of University Culture - Focused on the Commuting Patterns - (2000)

The purpose of this study is to compare the living cultures among three types of undergraduate students, grouped by commuting patterns, attending universities in Chung-Cheong Do: a long-distance type, a short-distance type, and a living-alone type. The survey was performed with questionnaires and the subjects were 1167 undergraduate students. The results are as follows: for a long-distance type, the levels of housing environments and consumption expenditures were relatively high, but the students felt constrainted by the commuting time. For a short-distance type, the consensus in decision-making with parents and the degree of conflict reconciliation were the lowest. For a living-alone type, the levels of housing environments and consumption expenditures were relatively poorer, but the students spent relative]y more time at school and the attitudes of school and department which they belong to were relatively higher.
Production of Recombinant Adeno‐Associated Viral Vectors for In Vitro and In Vivo Use (2007)

Adeno-associated virus is a nonpathogenic human virus that has been developed into a gene-delivery vector due to its high efficiency of infection in many different cell types and its ability to persist and lead to long-term gene expression. The vector is also a valuable tool in molecular biology experiments. This unit describes efficient methods to generate high-titer, research-grade, adenovirus-free, recombinant single-stranded and self-complementary adeno-associated virus in various serotypes, along with methods to quantify the viral vectors.
Gene expression profiling predicts clinical outcome of prostate cancer (2004)

One of the major problems in management of prostate cancer is the lack of reliable genetic markers predicting the clinical course of the disease. We analyzed expression profiles of 12,625 transcripts in prostate tumors from patients with distinct clinical outcomes after therapy as well as metastatic human prostate cancer xenografts in nude mice. We identified small clusters of genes discriminating recurrent versus nonrecurrent disease with 90% and 75% accuracy in two independent cohorts of patients. We examined one group of samples (21 tumors) to discover the recurrence predictor genes and then validated the predictive power of these genes in a different set (79 tumors). Kaplan-Meier analysis demonstrated that recurrence predictor signatures are highly informative (P < 0.0001) in stratification of patients into subgroups with distinct relapse-free survival after therapy. A gene expression-based recurrence predictor algorithm was informative in predicting the outcome in patients with early-stage disease, with either high or low preoperative prostate-specific antigen levels and provided additional value to the outcome prediction based on Gleason sum or multiparameter nomogram. Overall, 88% of patients with recurrence of prostate cancer within 1 year after therapy were correctly classified into the poor-prognosis group. The identified algorithm provides additional predictive value over conventional markers of outcome and appears suitable for stratification of prostate cancer patients at the time of diagnosis into subgroups with distinct survival probability after therapy.
Multipotential Marrow Stromal Cells Transduced to Produce L -DOPA: Engraftment in a Rat Model of Parkinson Disease (1999)

Bone marrow stromal cells can be used as an alternative source of cells for neural transplantation and repair. Here, the efficacy of genetically modified marrow stromal cells was examined in a rat model of Parkinson disease. Rat marrow stromal cells (rMSCs) and human marrow stromal cells (hMSCs) were genetically engineered by transduction with retroviruses encoding tyrosine hydroxylase (TH) and GTP cyclohydrolase I, the enzyme necessary for production of the tetrahydrobiopterin cofactor for TH (BH4). Transduced cells synthesized 3,4-dihydroxyphenylalanine (L-DOPA) in vitro and maintained their multipotentiality after retroviral transduction. To examine the cells in vivo, transduced rMSCs were injected into the striatum of 6-hydroxydopamine-lesioned rats. L-DOPA and metabolites were detected by microdialysis in the denervated striatum of rats that received doubly transduced rMSCs. Also, there was a significant reduction in apomorphine-induced rotation when compared with controls. The cells engrafted and survived for at least 87 days. However, expression of the transgenes ceased at about 9 days, an observation consistent with reports from other laboratories in which similar retroviruses were used to express transgenes in the brain.
A Vibration-Based Electromagnetic Energy Harvester Using Mechanical Frequency Up-Conversion Method (2010)

This paper presents a new vibration-based electromagnetic energy harvester using a mechanical frequency up-conversion method for harvesting energy from external low-frequency vibrations within a range of 1-10 Hz. The structure consists of a magnet placed on a diaphragm, a polystyrene cantilever carrying a pick-up coil, and a mechanical barrier which converts low-frequency vibrations to a higher frequency, hence increasing the efficiency of the system. The tested structure proved to generate 88.6 mV and 544.7 μW rms power output by up-converting 10-Hz external vibration to 394 Hz. The obtained power density is 184 μW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , with a device volume of 2.96 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . An analytical model is developed to analyze the behavior of the energy harvester prototypes with various dimensions. The model predicts the performance parameters of the structures within 5% error range. The effect of scaling down the device dimensions is investigated through the developed model and fabricated prototypes. It is shown that the power density of the energy harvester is increased as its dimensions are scaled down, proving that the proposed structure is a good candidate to be used in low-power wireless microsystems operating at low-frequency vibrations.
Atherosclerotic Plaque Composition and Classification Identified by Coronary Computed Tomography (2013)

CT-derived Plaque Maps based on contrast-adjusted attenuation ranges can define individual plaque components with a similar accuracy to VH-IVUS ex vivo. However, coronary CT Plaque Maps could not reliably classify plaques and identify TCFA, such that high-risk plaques may be misclassified or overlooked.
The morphology of ligament insertions after failure at low strain velocity: an evaluation of ligament entheses in the rabbit knee. (1996)

The morphology of failed rabbit knee entheses is described after in vitro load to failure testing at low strain velocity. Avulsion fracture was the dominant failure mode both for the cruciate ligaments and the medial collateral ligament. The patellar ligament became avulsed in most cases from the patellar insertion. The ligamentous anterior attachment of the medial meniscus failed by a midsubstance rupture and the posterior fibrocartilaginous attachment by a rupture near to the meniscal horn. On histological inspection the failure characteristics usually appeared more elaborate, involving to different degrees all portions of the bone-ligament-bone complexes. Avulsion fracture through subchondral bone was often combined with a partial ligament midsubstance rupture. In few cases avulsion from the cement line was combined with a rupture between the uncalcified fibrocartilage and the ligament. The medial collateral ligament failed in one case entirely at the cement line of its femoral insertion. Horizontal rupture through the calcified fibrocartilage and a vertical cleavage crossing the tidemark were also observed. The superficial portion of the patellar ligament failed with a midsubstance rupture, and the deeper part with an avulsion through the calcified fibrocartilage or an avulsion fracture. The complex failure characteristics may be attributed to uneven loading, nonuniformity of the structure, and specific anatomical location. Subchondral bone beneath femoral and tibial insertions seems to be weaker than the transitional zone between soft tissue and hard bone at the enthesis. The overall inferior structural quality of a ruptured ligament has to be taken into account when parts of the original structure are used for suturing or reconstruction.
Tuning the threshold voltage of organic field-effect transistors by an electret encapsulating layer (2007)

Here, the authors present a technique to adjust the threshold voltage of an organic field-effect transistor (OFET) using a design similar to a dual-gate structure with an insulating Teflon-based electret layer as a second gate. The threshold voltage of a pentacene bottom gate OFET was shifted from +13.1to−2.3V by depositon of a 1.7μm thick electret layer, proving the principal feasibility of this approach. This controlled tuning of the threshold voltage compensates one of the main drawbacks of organic electronics and even allows switching from a depletion to an enhancement-type transistor behavior.
Ionic polarization-induced current–voltage hysteresis in CH3NH3PbX3 perovskite solar cells (2016)

CH3NH3PbX3 (MAPbX3) perovskites have attracted considerable attention as absorber materials for solar light harvesting, reaching solar to power conversion efficiencies above 20%. In spite of the rapid evolution of the efficiencies, the understanding of basic properties of these semiconductors is still ongoing. One phenomenon with so far unclear origin is the so-called hysteresis in the current-voltage characteristics of these solar cells. Here we investigate the origin of this phenomenon with a combined experimental and computational approach. Experimentally the activation energy for the hysteretic process is determined and compared with the computational results. First-principles simulations show that the timescale for MA(+) rotation excludes a MA-related ferroelectric effect as possible origin for the observed hysteresis. On the other hand, the computationally determined activation energies for halide ion (vacancy) migration are in excellent agreement with the experimentally determined values, suggesting that the migration of this species causes the observed hysteretic behaviour of these solar cells.
Arabidopsis LHT1 Is a High-Affinity Transporter for Cellular Amino Acid Uptake in Both Root Epidermis and Leaf Mesophyll (2006)

Amino acid transport in plants is mediated by at least two large families of plasma membrane transporters. Arabidopsis thaliana, a nonmycorrhizal species, is able to grow on media containing amino acids as the sole nitrogen source. Arabidopsis amino acid permease (AAP) subfamily genes are preferentially expressed in the vascular tissue, suggesting roles in long-distance transport between organs. We show that the broad-specificity, high-affinity amino acid transporter LYSINE HISTIDINE TRANSPORTER1 (LHT1), an AAP homolog, is expressed in both the rhizodermis and mesophyll of Arabidopsis. Seedlings deficient in LHT1 cannot use Glu or Asp as sole nitrogen sources because of the severe inhibition of amino acid uptake from the medium, and uptake of amino acids into mesophyll protoplasts is inhibited. Interestingly, lht1 mutants, which show growth defects on fertilized soil, can be rescued when LHT1 is reexpressed in green tissue. These findings are consistent with two major LHT1 functions: uptake in roots and supply of leaf mesophyll with xylem-derived amino acids. The capacity for amino acid uptake, and thus nitrogen use efficiency under limited inorganic N supply, is increased severalfold by LHT1 overexpression. These results suggest that LHT1 overexpression may improve the N efficiency of plant growth under limiting nitrogen, and the mutant analyses may enhance our understanding of N cycling in plants.
Interactive Visualization and Analysis of Network and Sensor Data on Mobile Devices (2006)

Mobile devices are rapidly gaining popularity due to their small size and their wide range of functionality. With the constant improvement in wireless network access, they are an attractive option not only for day to day use. but also for in-field analytics by first responders in widespread areas. However, their limited processing, display, graphics and power resources pose a major challenge in developing effective applications. Nevertheless, they are vital for rapid decision making in emergencies when combined with appropriate analysis tools. In this paper, we present an efficient, interactive visual analytic system using a PDA to visualize network information from Purdue's Ross-Ade Stadium during football games as an example of in-held data analytics combined with text and video analysis. With our system, we can monitor the distribution of attendees with mobile devices throughout the stadium through their access of information and association/disassociation from wireless access points, enabling the detection of crowd movement and event activity. Through correlative visualization and analysis of synchronized video (instant replay video) and text information (play statistics) with the network activity, we can provide insightful information to network monitoring personnel, safety personnel and analysts. This work provides a demonstration and testbed for mobile sensor analytics that will help to improve network performance and provide safety personnel with information for better emergency planning and guidance
Differential effects of glycoprotein B epitope-specific antibodies on human cytomegalovirus-induced cell-cell fusion (2003)

Attachment of, and cell-cell fusion induced by, human cytomegalovirus were studied in the presence of neutralizing monospecific antibodies against antigenic domains 1 (AD-1) or 2 (AD-2) of glycoprotein B (gB, gpUL55). Efficient inhibition of the virion-mediated fusion event was consistently observed for the human AD-2-specific antibody as determined by a reporter gene activation assay based on permissive astrocytoma cells. In contrast, antibodies directed against the major neutralizing gB epitope AD-1 reduced fusion only by 20-60 %. Virus attachment via heparan sulfate was unaffected by the antibodies under the conditions used. Virus receptor binding as examined by heparin treatment of adsorbed virus was significantly reduced only if the virus had been coated with the AD-2-specific antibody. Neutralization of virus infectivity by the AD-2-specific antibody thus seems most likely to result from interference with a receptor-binding event during initial virus-host cell interaction.
Assessment of the feasibility of exon 45–55 multiexon skipping for duchenne muscular dystrophy (2008)

We conclude that current state of the art does not sufficiently support clinical development of multiexon skipping for DMD.
Protection against pneumococcal infection in mice conferred by phosphocholine-binding antibodies: specificity of the phosphocholine binding and relation to several types (1983)

Some anti-phosphocholine antibodies protect mice against challenge with certain, but not all, pneumococcal types. We found that both their isotype and reactivity with the cell wall C-polysaccharide of encapsulated pneumococci, as measured by immunodiffusion, were important in predicting the protective activity of anti-phosphocholine antibodies. We propose that the specificity of the protective antibodies includes the backbone of the phosphocholine-containing structure.
Suppression of tumorigenicity in human teratocarcinoma cell line PA-1 by introduction of chromosome 4. (1994)

Teratocarcinomas are tumors that develop spontaneously in the gonads and usually contain a rapidly dividing, undifferentiated stem cell population. Immature ovarian teratocarcinomas are highly malignant with only 30-60% of patients surviving for 2 years after diagnosis. We have used microcell fusion to introduce individually tagged normal human chromosomes into the PA-1 human teratocarcinoma cell line. Introduction of human chromosome 4 caused a cell morphology in culture and suppressed PA-1 tumorigenicity in nude mice, whereas addition of portions of either chromosome 7 or 12 had no effect on the cell phenotype. The PA-1 cell line regained its tumorigenicity when the tagged chromosome 4 was lost under negative selection. We conclude that there is a putative tumor suppressor gene on human chromosome 4 whose expression interferes with the tumorigenicity of PA-1 cells.