gebhart/patrepeval huggingface dataset:
F508 amino acid deletion mutation of CFTR gene in Korean lung cancer patients (2001)

Mutations of the transmembrane conductance regulator (CFTR) gene in cystic fibrosis lead to dysfunction of the lung, pancreas, and sweat glands, etc. To investigate the possibility of the relationship between lung cancer and the mutations of CFTR gene, we determined amino acid sequences using reverse transcription-polymerase chain reaction (RT-PCR) and DNA sequencing. In this study, the deletion mutation of 508th amino acid in one of nine lung caner patients was found confirming that CFTR gene mutation exists in a Korean lung cancer patient.
Validation of a High-Throughput Liquid Chromatography–Tandem Mass Spectrometry Method for Urinary Cortisol and Cortisone (2002)

The sensitivity and specificity of the LC-MS/MS method for urinary free cortisol and cortisone offer advantages over routine immunoassays or chromatographic methods because of elimination of drug interferences, high throughput, and short chromatographic run time.
Synthesis and Binding Properties of Oligonucleotides Containing an Azobenzene Linker (1998)

Abstract Incorporation of an azobenzene-4,4′-diamide group via a linker arm into the 3′-hydroxyl function of one oligonucleotide segment and the 5′-OH of other oligonucleotide has been described. The binding of the oligonucleotides containing the azobenzene linker was investigated by UV melting behaviors. The azobenzene linker has been shown to be useful as an effective bridge for stabilizing hairpin duplex and triplex.
Microbial metabolism of anthracycline antibiotics daunomycin and adriamycin. (1978)

It has been shown that the antitumor antibiotics daunomycin (1) and adriamycin (4) are metabolized by microorganisms in a fashion similar to their metabolism by mammalian cells. Both the fungus Mucor spinosus and its cell-free extracts reduce the 13-keto group of daunomycin to give daunomycinol (2) by a TPNH-dependent process. Cell-free extracts of Streptomyces steffisburgensis convert adriamycin and daunomycinol to their 7-deoxyaglycones (5) and (3) by DPNH-linked reductive glycosidic cleavage. Cell-free extracts of the latter organism convert 7-deoxyadriamycinone (5) to 7-deoxyadriamycinol aglycone (6) by TPNH-linked 13-keto reduction.
Improved targeting of an anti-epidermal growth factor receptor variant III monoclonal antibody in tumor xenografts after labeling using N-succinimidyl 5-iodo-3-pyridinecarboxylate. (1997)

Monoclonal antibody (mAb) L8A4, specific for the tumor-associated mutant epidermal growth factor receptor variant III (EGFRvII), is internalized and degraded after cell binding. Four paired-label experiments were performed in athymic mice bearing EGFRvIII-positive xenografts to determine the suitability of N-succinimidyl 3-iodo-5-pyridinecarboxylate (SIPC) for labeling this internalizing mAb. In mice with HC2 20 d2 xenografts, tumor uptake reached a maximum of 32.7 +/- 2.0% injected dose/g when labeled using SIPC, a value significantly higher (P < 0.05, paired t test) than that observed when L8A4 was labeled using lodogen (24.4 +/- 2.2% injected dose/g). The specificity of mAb uptake in HC2 20 d2 and U87MG(delta)EGFR xenografts was measured in separate experiments by coadministration of L8A4 and nonspecific, isotype-matched P3X63Ag8 mAb, both radioiodinated using SIPC. Tumor localization indices were approximately 10 or more by 72 h, a degree of specificity 3-4 times higher than that reported previously when labeling was performed using the tyramine cellobiose (TCB) method. In a final study directly comparing L8A4 labeled using SIPC and TCB, similar tumor levels were obtained (SIPC, 33.7 +/- 6.1% injected dose/g at 24 h; TCB, 37.8 +/- 6.7% injected dose/g at 24 h); however, tumor-to-tissue ratios for the liver, spleen, and kidneys were 3 times higher with SIPC at later time points. These results suggest that SIPC is a promising method for labeling this anti-EGFRvIII mAb and possibly other mAbs that internalize after binding.
Connective Tissue Growth Factor (1997)

Connective tissue growth factor (CTGF) is a novel cysteine-rich, secreted peptide, which is implicated in human atherosclerosis and fibrotic disorders such as systemic scleroderma. CTGF is a member of the peptide family that includes serum-induced immediate early gene products, a v-src-induced peptide, and a putative proto-oncogene. The CTGF gene family is a modular protein and is conserved throughout evolution. CTGF mRNA has been found in the human, mouse, chicken, frog, and fly. The functions of the CTGF gene family include embryogenesis, wound healing, and regulation of extracellular matrix production. Human CTGF is undetectable in normal blood vessels but overexpressed in atherosclerotic lesions, suggesting an important role in atherogenesis.
Architecture of centralized field-configurable memory (1995)

As the capacities of FPGAs grow, it becomes feasible to implement the memory portions of systems directly on an FPGA together with logic. We believe that such an FPGA must contain specialized architectural support in order to implement memories efficiently. The key feature of such architectural support is that it must be flexible enough to accommodate many different memory shapes (widths and depths) as well as allowing different numbers of independently-addressed memory blocks. This paper describes a family of centralized Field-Configurable Memory architectures which consist of a number of memory arrays and dedicated mapping blocks to combine these arrays. We also present a method for comparing these architectures, and use this method to examine the tradeoffs involved in choosing the array size and mapping block capabilities.
An Investigation of the Expression of G1-Phase Cell Cycle Proteins in Focal Cortical Dysplasia Type IIB (2007)

Balloon cells (BCs) are the pathologic hallmark of focal cortical dysplasia type IIB, a common cause of pharmacoresistent epilepsy. Expression of markers of cell immaturity and of the proliferation marker minichromosome maintenance protein 2 (mcm2) have been previously shown in BCs, suggesting that these cells might represent a pool of less-differentiated cells licensed for replication. An alternative explanation is that these cells are the remnants of early cortical plate cells that have failed to differentiate or to be eliminated during development and are arrested in the cell cycle, a hypothesis that this study aims to explore. Using immunohistochemical methods and semiquantitative analysis in 19 cases of focal cortical dysplasia (ages 1-81 years), we studied the expression of cell cycle proteins important either in regulating progression through the G1 phase or inducing cell arrest and promoting premature senescence. Only a small fraction of BCs expressed geminin, suggesting that few BCs enter the S phase or complete the cell cycle. Variable expression of nonphosphorylated retinoblastoma protein (Rb), cdk4, and p53 was noted in BCs. Cyclin E, D1, cdk2, phosphorylated Rb (795 and 807/811), and checkpoint 2 expression levels were low in BCs. These findings suggest early rather than late G1 arrest. Cell senescence could be induced by an undefined cerebral insult during development or alternatively represent a physiologic replicative senescence. These findings also suggest that dysregulation of cell cycle pathways may occur in focal cortical dysplasia, which opens further areas for exploration as potential new treatment avenues.
Switched-source-impedance CMOS circuit for low standby subthreshold current giga-scale LSI's (1993)

A switched-source-impedance (SSI) CMOS circuit is proposed as a means of reducing the exponential increase of subthreshold current with threshold-voltage scaling. Inserting a switched impedance at the source of a MOS transistor reduces the standby subthreshold current of giga-scale LSI's operating at room temperature by three to four orders of magnitude and suppresses the current variation caused by threshold-voltage and temperature fluctuations. The scheme is applicable to any combinational and sequential CMOS logic circuits as long as their standby node voltages are predictable. The standby current of a 16-Gb DRAM is expected to be reduced from 1.1 A to 0.29 mA using this scheme. Hence, battery backup of giga-scale LSI's will be possible even at room temperature and above.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Rational design of peptides active against the gram positive bacteria Staphylococcus aureus (2008)

In an attempt to increase the antimicrobial activity of the insect defensin from Anopheles gambiae, which is active against Staphylococcus aureus at low concentration, hybrid defensins were designed by combining conserved sequence regions and variable regions of insect defensins. Their activity against S. aureus strains sensitive and resistant to conventional antibiotics was evaluated, and the toxicity of the most active molecules was tested. The three-dimensional structure of Anopheles gambiae defensin and five hybrids were determined by NMR and molecular modelling. This strategy led to the design of two chimeric defensins with increased activity compared with the native molecule, but one of them appears to be toxic to mice at a rather low concentration. The structure of the CS alphabeta motif, which is a characteristic of insect defensin, is sensitive to sequence modifications, in particular in the N-terminal loop. The existence of the CS alphabeta is most probably a prerequisite for the stability and the activity of the molecule, but is not sufficient by itself since the hybrid displaying the best defined structure is not active against the tested strains. The analysis of the structure, in relation with the activity and the toxicity data, underlines the importance of turns and of the N-terminal loop. Residues located in the turns contributing to the preservation of positive electrostatic areas at the surface of the molecules seem particularly important for the activity of the molecule, while residues involved in the N-terminal loop are both involved in the modulation of the activity and the toxicity of the molecule.
Nitrate-induced photooxidation of trace organic chemicals in water (1987)

The oxidation kinetics of butyl chloride, nitrobenzene, anisole, and methylmercury in the presence of hydroxyl radical (&lt;sup&gt;&lt;B&gt;·&lt;/B&gt;&lt;/sup&gt;OH) scavengers were used to determine the rate and quantum efficiency for production of &lt;sup&gt;&lt;B&gt;·&lt;/B&gt;&lt;/sup&gt;OH from irradiated nitrate ions in water. The experiments were conducted under steady-state irradiations with monochromatic radiation (313 nm) and with sunlight. The mean quantum efficiency for &lt;sup&gt;&lt;B&gt;·&lt;/B&gt;&lt;/sup&gt;OH production at 313 nm rises from 0.013 ± 0.002 at 20 °C to 0.017 ± 0.003 at 30 °C in the pH range 6.2-8.2. Results of this study are used to estimate nitrate-induced photooxidation rates of trace organic chemicals under a variety of environmental conditions.
Effect of size and geographic origin of Aedes aegypti on oral infection with dengue-2 virus. (1998)

Differences in larval habitats cause variation in the size of Aedes aegypti (L.) adults. We suspected that such size variation was related to the ease with which the mosquitoes could be infected with dengue virus. Using a rearing procedure that produced three distinct size classes of mosquitoes, we determined the percentage of mosquitoes that developed disseminated dengue-2 infection following oral feeding with a suspension containing 3.3 x 10(7) plaque-forming units/ml. Mosquitoes were reared from eggs deposited by females captured in either of two villages in Chachoengsao Province or in Bangkok, Thailand. More of the larger mosquitoes (10.7%) were infected than the medium (5.6%) or small (5.7%) mosquitoes. Mosquitoes from Bangkok were less easily infected (5.0%) than mosquitoes from either of the two villages (8.5% and 10.7%). These results suggest that quantitative risk assessment of dengue transmission may be very difficult unless inoculation rate is measured directly. Also, control procedures that reduce density of larvae in individual containers may exacerbate dengue transmission by creating larger mosquitoes that are more easily infected.
Idiotypic Networks and Other Preconceived Ideas (1984)

The preceding section implies that the immune system (like the brain) reflects first ourselves, then produces a reflection of this reflection, and that subsequently it reflects the outside world: a hall of mirrors. The second mirror images (i.e., stable anti-idiotypic elements) may well be more complex than the first images (i.e., anti-self). Both give rise to distortions (e.g., mutations, gene rearrangements) permitting the recognition of nonself. The mirror images of the outside world, however, do not have permanency in the genome. Every individual must start with self. Paraphrasing Nicolas Schöffer (Schöffer 1982): those who always seek exterior pressures (e.g., microbes) to account for the evolution of the sets of V genes, would do well to turn their vision towards the interiors of themselves, and there discover the mystery, perhaps never completely revealable, of the immune system.
The influenza virus NS1 protein: a novel inhibitor of pre-mRNA splicing. (1994)

We have shown previously that the influenza virus NS1 protein inhibits the nuclear export of mRNAs. Here we demonstrate that the NS1 protein also regulates another post-transcriptional step: It inhibits pre-mRNA splicing both in vivo and in vitro. The mode by which the NS1 protein inhibits pre-mRNA splicing is novel. The pre-mRNA forms spliceosomes, but subsequent catalytic steps in splicing are inhibited. Affinity selection experiments establish that the NS1 protein is associated with the spliceosomes that are formed. The RNA-binding domain of the NS1 protein is required for the inhibition of splicing and for the interaction of the protein with spliceosomes. Because the NS1 protein is associated with U6 snRNA in influenza virus-infected cells as well as in splicing extracts from uninfected cells, it is likely that the NS1 protein also inhibits pre-mRNA splicing in infected cells. Surprisingly, the splicing of the viral ns1 mRNA, the very mRNA that encodes the NS1 protein, was resistant to inhibition by the NS1 protein. This resistance is conferred by sequences in ns1 mRNA.
Principles of pharmacology (2013)

Principles of pharmacology : , Principles of pharmacology : , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
[Heterogeneity of polyadenylation site of mRNA coding for human serum albumin]. (1990)

Human fetal liver cDNA was cloned in pBR322 vector by dG:dC-tailing method. The cDNA library was screened for liver-specific clones by means of differential hybridization. Human fetal liver and human kidney cDNAs were used as hybridization probes. Application of this procedure revealed twenty five liver-specific clones among about one thousand recombinants analysed. These clones represent cDNAs corresponding abundant mRNAs. Eighteen clones were identified as encoding serum albumin. Two different mRNA polyadenylation sites were found in four sequenced plasmids. Cleavage/polyadenylation site in two plasmids, pHA1 and pHA12, is situated fifteen nucleotides downstream the AATAAA signal; in two other plasmids, pHA8 and pHA25, this site is ten nucleotides downstream the same signal.
FD-TD modeling of digital signal propagation in 3-D circuits with passive and active loads (1994)

Most existing computer-aided circuit design tools are limited when digital clock speeds exceed several hundred MHz. These tools may not deal effectively with the physics of UHF and microwave electromagnetic wave energy transport along metal surfaces such as ground planes or in the air away from metal paths that are common at or above this frequency range. In this paper, we discuss full-wave modeling of electronic circuits in three dimensions using the finite-difference time-domain (FD-TD) solution of Maxwell's equations. Parameters such as stripline complex line impedance, propagation constant, capacitance per unit length and inductance per unit length can be easily computed as a function of frequency. We also discuss FD-TD Maxwell's equations computational modeling of lumped-circuit loads and sources in 3-D, including resistors and resistive voltage sources, capacitors, inductors, diodes, and transistors. We believe that this approach will be useful in simulating the large-signal behavior of very high-speed nonlinear analog and digital devices in the context of the full-wave time-dependent electromagnetic field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Engraftment and Differentiation of Human Metanephroi into Functional Mature Nephrons after Transplantation into Mice Is Accompanied by a Profile of Gene Expression Similar to Normal Human Kidney Development (2002)

Metanephroi, the embryonic precursors of the adult kidney, can be induced in vivo to grow and develop. Despite their potential clinical utility for transplantation, the ability of human metanephroi to differentiate after transplantation into functional mature nephrons is mostly unknown. To address this, 70-d human metanephroi were transplanted into NOD/SCID mice; global gene expression patterns that underlie development of human metanephric transplants were analyzed and compared with normal human kidney development. In addition, functionality of the grafts was assessed by dimercaptosuccinic acid radioisotope scans at different times after transplantation. The results of hybridization to cDNA arrays when RNA was derived from normal human kidneys at 8, 12, 16, and 20 wk gestation demonstrated that a subset of 240 genes changed substantially with time. The induced genes can be classified as cell cycle regulators, transcription and growth factors, and signaling, transport, adhesion, and extracellular matrix molecules. Strikingly, clustering analysis of global gene expression at 2, 6, and 10 wk after metanephric transplantation revealed an expression profile that characterizes normal human kidney development. Moreover, maturation of the transplants was accompanied by an increased uptake of dimercaptosuccinic acid. Nevertheless, expression levels of specific genes were mostly found to be suppressed in the transplants compared with the normal kidneys. These data provide insights into human kidney development and support the possibility of the transplantability of human metanephroi. Understanding of the molecular regulation of the transplanted developing metanephroi might lead to the development of strategies aimed at increasing the levels of specific genes, nephron endowment, and graft function.
Targeting Endothelial Cells Overexpressing VEGFR-2:  Selective Toxicity of Shiga-like Toxin−VEGF Fusion Proteins (2001)

Growing endothelial cells at the sites of angiogenesis express high numbers of VEGF receptors and therefore may be particularly sensitive to VEGF-mediated drug delivery. To test this hypothesis we have constructed a protein containing the catalytic A-subunit of Shiga-like toxin I fused to VEGF121 (SLT-VEGF/L). Wild-type A-subunit is a site-specific N-glycosidase of 28S rRNA that inhibits protein synthesis after being delivered into cells by separate cell-binding B-subunits. SLT-VEGF/L retains functional activities of both SLT and VEGF121 moieties, since it inhibits protein synthesis in a cell-free translation system and induces VEGFR-2 tyrosine autophosphorylation. SLT-VEGF/L selectively inhibits growth of porcine endothelial cells expressing 2.5 x 10(5) VEGFR-2/cell with an IC50 of 0.2 nM and rapidly induces apoptosis at concentrations >1 nM. We found that sensitivity of VEGFR-2 transfected PAE cells to SLT-VEGF/L declined as the cellular VEGFR-2 density decreased; PAE cells expressing 25000 VEGFR-2/cell were as sensitive as parental cells lacking the receptor. Growth inhibition and induction of apoptosis by SLT-VEGF/L require intrinsic N-glycosidase activity of the SLT moiety, but take place without significant inhibition of protein synthesis. Selective cytotoxicity of SLT-VEGF/L against growing endothelial cells overexpressing VEGFR-2 suggests that it may be useful in targeting similar cells at the sites of angiogenesis.
TREATMENT WITH INTERLEUKIN-4 PROLONGS ALLOGENEIC NEONATAL HEART GRAFT SURVIVAL BY INDUCING T HELPER 2 RESPONSES (1998)

rIL-4 therapy markedly prolonged neonatal cardiac allograft survival, and, with anti-CD4 therapy, it further prolonged survival. It induced IL-4 mRNA in lymphoid tissues and enhanced alloantibody production, especially IgG1, which demonstrated enhanced Th2 responses, but did not affect Th1 cytokines.
Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: Need for new phenomenological models for solventogenesis and butanol inhibition? (2000)

Two metabolic engineering tools, namely gene inactivation and gene overexpression, were employed to examine the effects of two genetic modifications on the fermentation characteristics of Clostridium acetobutylicum. Inactivation of the butyrate kinase gene (buk) was examined using strain PJC4BK, while the combined effect of buk inactivation and overexpression of the aad gene—encoding the alcohol aldehyde dehydrogense (AAD) used in butanol formation—was examined using strain PJC4BK(pTAAD). The two strains were characterized in controlled pH ≥ 5.0 fermentations, and by a recently enhanced method of metabolic flux analysis. Strain PJC4BK was previously genetically characterized, and fermentation experiments at pH ≥ 5.5 demonstrated good, but not exceptional, solvent-production capabilities. Here, we show that this strain is a solvent superproducer in pH ≥ 5.0 fermentations producing 225 mM (16.7 g/L) of butanol, 76 mM of acetone (4.4 g/L), and 57 mM (2.6 g/L) of ethanol. Strain PJC4BK(pTAAD) produced similar amounts of butanol and acetone but 98 mM (4.5 g/L) of ethanol. Both strains overcame the 180 mM (13 g/L) butanol toxicity limit, without any selection for butanol tolerance. Work with strain PJC4BK(pTAAD) is the first reported use of dual antibiotic selection in C. acetobutylicum. One antibiotic was used for selection of strain PJC4BK while the second antibiotic selected for the pTAAD presence. Overexpression of aad from pTAAD resulted in increased ethanol production but did not increase butanol titers, thus indicating that AAD did not limit butanol production under these fermentation conditions. Metabolic flux analysis showed a decrease in butyrate formation fluxes by up to 75% and an increase in acetate formation fluxes of up to 100% during early growth. The mean specific butanol and ethanol formation fluxes increased significantly in these recombinant strains, up to 300% and 400%, respectively. Onset of solvent production occurred during the exponential-growth phase when the culture optical density was very low and when total and undissociated butyric acid levels were <1 mM. Butyrate levels were low throughout all fermentations, never exceeding 20 mM. Thus, threshold butyrate concentrations are not necessary for solvent production in these stains, suggesting the need for a new phenomenological model to explain solvent formation. © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng 67: 1–11, 2000.