gebhart/patrepeval huggingface dataset:
Quantification of splice variants using real-time PCR (2001)

A reliable and robust method for measuring the expression of alternatively spliced transcripts is an important step in investigating the significance of each variant. So far, accurate quantification of splice variants has been laborious and difficult due to the intrinsic limitations of conventional methods. The many advantages of real-time PCR have made this technique attractive to study its application in quantification of splice isoforms. We use skipping of exon 37 in the NF1 gene as a model to compare and evaluate the different strategies for quantitating splice variants using real-time PCR. An overview of three different possibilities for detecting alternative transcripts is given. We propose the use of a boundary-spanning primer to quantify isoforms that differ greatly in abundance. We describe here a novel method for creating a reliable standard curve using one plasmid containing both alternative transcripts. In addition, we validate the use of an absolute standard curve based on a dilution series of fluorometrically quantified PCR products.
Human GRB-IRβ/GRB10 (1997)

cDNA clones encoding human (h) Grb7 and a previously unknown protein with high homology to hGrb-IR and mGrb10 (where m indicates mouse) were found by screening expressed sequence tag data bases. hGrb7 mRNA expression is greatest in pancreas and restricted to a few other tissues. The second protein termed hGrb-IRbeta/Grb10 contains an intact PH domain and lacks the 80-residue mGrb10 insertion. Expression is greatest in pancreas and muscle but occurs in nearly all tissues. hGrb-IRbeta/Grb10 and hGrb-IR likely arise as alternative mRNA splicing products of a common gene. Reverse transcriptase-coupled polymerase chain reaction shows both mRNAs in muscle. In cells, Grb-IRbeta/Grb10 protein translocates from cytosol to membrane upon insulin stimulation, most likely due to direct interactions with the insulin receptor. These interactions are mediated by the SH2 domain and additional regions of the protein. Studies with mutated receptors and synthetic phosphopeptides show that the hGrb-IRbeta/Grb10 SH2 domain binds at least two sites in the insulin receptor: the kinase activation loop > the juxtamembrane site. hGrb-IRbeta/Grb10 also binds a 135-kDa phosphoprotein in unstimulated 3T3-L1 adipocytes; binding is reduced upon insulin stimulation. In addition, the c-Abl SH3 domain binds Grb-IR/Grb10, whereas Fyn, phosphatidylinositol 3-kinase p85, and Grb2 SH3 domains do not. The site of c-Abl SH3 domain interaction is highly conserved within the Grb-IR/Grb10/Grb7/Grb14 family. hGrb-IRbeta/Grb10 also binds platelet-derived growth factor and epidermal growth factor receptors, suggesting a broader role in the signaling pathways of numerous receptors. We conclude that hGrb-IRbeta/Grb10 is a widely expressed, PH and SH2 domain-containing, SH3 domain-binding protein that functions downstream from activated insulin and growth factor receptors.
SJG-136 (NSC 694501), A Novel Rationally Designed DNA Minor Groove Interstrand Cross-Linking Agent with Potent and Broad Spectrum Antitumor Activity (2004)

Abstract Pyrrolo[2,1-c][1,4]benzodiazepine dimer SJG-136 (NSC 694501) selectively cross-links guanine residues located on opposite strands of DNA, and exhibits potent in vitro cytotoxicity. In addition, SJG-136 is highly active in vivo in hollow fiber assays. In the current investigation, SJG-136 was evaluated for in vivo efficacy in 10 tumor models selected on the basis of sensitivity of cells grown in the hollow fiber and in vitro time course assays: LOX IMVI and UACC-62 (melanomas); OVCAR-3 and OVCAR-5 (ovarian carcinomas); MDA-MB-435 (breast carcinoma); SF-295 and C-6 (gliomas); LS-174T (colon carcinoma); HL-60 TB (promyelocytic leukemia); and NCI-H522 (lung carcinoma). SJG-136 was active against small (150 mg) and large (250–400 mg) xenografts with tumor mass reductions in all 10 models. In addition, significant growth delays occurred in nine models, cell kill in six models ranged between 1.9 and 7.2 logs, and there were 1 to 4/6 tumor-free responses in six models. SJG-136 is active following i.v. bolus injections, as well as by 5-day continuous infusions. Of all of the schedules tested, bolus administrations for 5 consecutive days (qd×5) conferred the greatest efficacy. SJG-136 is active over a wide dosage range in athymic mouse xenografts: on a qd×5 schedule, the maximum-tolerated dose was ∼120 μg/kg/dose (total dose: 0.6 mg/kg = 1.8 mg/m2) and the minimum effective dose in the most sensitive model (SF-295) was ∼16 μg/kg/dose (total dose: 0.08 mg/kg = 0.24 mg/m2). Results of this study extend the initial in vivo observations reported in the reference above and confirm the importance of expediting more detailed preclinical evaluations on this novel agent in support of phase I clinical trials in the United Kingdom and the United States, which are planned to commence shortly.
A New Class of PSMA-617-Based Hybrid Molecules for Preoperative Imaging and Intraoperative Fluorescence Navigation of Prostate Cancer (2022)

The development of PSMA-targeting low-molecular-weight hybrid molecules aims at advancing preoperative imaging and accurate intraoperative fluorescence guidance for improved diagnosis and therapy of prostate cancer. In hybrid probe design, the major challenge is the introduction of a bulky dye to peptidomimetic core structures without affecting tumor-targeting properties and pharmacokinetic profiles. This study developed a novel class of PSMA-targeting hybrid molecules based on the clinically established theranostic agent PSMA-617. The fluorescent dye-bearing candidates of the strategically designed molecule library were evaluated in in vitro assays based on their PSMA-binding affinity and internalization properties to identify the most favorable hybrid molecule composition for the installation of a bulky dye. The library's best candidate was realized with IRDye800CW providing the lead compound. Glu-urea-Lys-2-Nal-Chx-Lys(IRDye800CW)-DOTA (PSMA-927) was investigated in an in vivo proof-of-concept study, with compelling performance in organ distribution studies, PET/MRI and optical imaging, and with a strong PSMA-specific tumor uptake comparable to that of PSMA-617. This study provides valuable insights about the design of PSMA-targeting low-molecular-weight hybrid molecules, which enable further advances in the field of peptidomimetic hybrid molecule development.
Identification and functional expression of a second human β‐galactoside α2,6‐sialyltransferase, ST6Gal II (2003)

BLAST analysis of the human and mouse genome sequence databases using the sequence of the human CMP-sialic acid:beta-galactoside alpha-2,6-sialyltransferase cDNA (hST6Gal I, EC2.4.99.1) as a probe allowed us to identify a putative sialyltransferase gene on chromosome 2. The sequence of the corresponding cDNA was also found as an expressed sequence tag of human brain. This gene contained a 1590 bp open reading frame divided in five exons and the deduced amino-acid sequence didn't correspond to any sialyltransferase already known in other species. Multiple sequence alignment and subsequent phylogenic analysis showed that this new enzyme belonged to the ST6Gal subfamily and shared 48% identity with hST6Gal-I. Consequently, we named this new sialyltransferase ST6Gal II. A construction in pFlag vector transfected in COS-7 cells gave raise to a soluble active form of ST6Gal II. Enzymatic assays indicate that the best acceptor substrate of ST6Gal II was the free disaccharide Galbeta1-4GlcNAc structure whereas ST6Gal I preferred Galbeta1-4GlcNAc-R disaccharide sequence linked to a protein. The alpha2,6-linkage was confirmed by the increase of Sambucus nigra agglutinin-lectin binding to the cell surface of CHO transfected with the cDNA encoding ST6Gal II and by specific sialidases treatment. In addition, the ST6Gal II gene showed a very tissue specific pattern of expression because it was found essentially in brain whereas ST6Gal I gene is ubiquitously expressed.
Discovery of a Potent, Orally Active 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitor for Clinical Study: Identification of (S)-2-((1S,2S,4R)-Bicyclo[2.2.1]heptan-2-ylamino)-5-isopropyl-5-methylthiazol-4(5H)-one (AMG 221) (2010)

Thiazolones with an exo-norbornylamine at the 2-position and an isopropyl group on the 5-position are potent 11beta-HSD1 inhibitors. However, the C-5 center was prone to epimerization in vitro and in vivo, forming a less potent diastereomer. A methyl group was added to the C-5 position to eliminate epimerization, leading to the discovery of (S)-2-((1S,2S,4R)-bicyclo[2.2.1]heptan-2-ylamino)-5-isopropyl-5-methylthiazol-4(5H)-one (AMG 221). This compound decreased fed blood glucose and insulin levels and reduced body weight in diet-induced obesity mice.
Synthetic amphipathic helical peptides promote lipid efflux from cells by an ABCA1-dependent and an ABCA1-independent pathway (2003)

In order to examine the necessary structural features for a protein to promote lipid efflux by the ABCA1 transporter, synthetic peptides were tested on ABCA1-transfected cells (ABCA1 cells) and on control cells. L-37pA, an l amino acid peptide that contains two class-A amphipathic helices linked by proline, showed a 4-fold increase in cholesterol and phospholipid efflux from ABCA1 cells compared to control cells. The same peptide synthesized with a mixture of l and d amino acids was less effective than L-37pA in solubilizing dimyristoyl phosphatidyl choline vesicles and in effluxing lipids. In contrast, the 37pA peptide synthesized with all d amino acids (D-37pA) was as effective as L-37pA. Unlike apoA-I, L-37pA and D-37pA were also capable, although at a reduced rate, of causing lipid efflux independent of ABCA1 from control cells, Tangier disease cells, and paraformaldehyde fixed ABCA1 cells. The ability of peptides to bind to cells correlated with their lipid affinity. In summary, the amphipathic helix was found to be a key structural motif for peptide-mediated lipid efflux from ABCA1, but there was no stereoselective requirement. In addition, unlike apoA-I, synthetic peptides can also efflux lipid by a passive, energy-independent pathway that does not involve ABCA1 but does depend upon their lipid affinity.
DOWNHOLE VIBRATION MONITORING & CONTROL SYSTEM (2003)

Testing of the prototype valve began during this quarter. The objective of the first preliminary tests was to determine the pressure drop that can be created across the valve under different conditions of flow and pressure. As described in Quarterly Report 3, the system uses pneumatic pressure to activate a cylinder which in turn loads two hydraulic cylinders containing the MR fluid. Testing was preformed with no sensors or gauges other than the air pressure supply gauge. The valve was powered at 36 volts and drew about 3.5 amps. The valve held back the MR fluid at 30 psi. (This is the air pressure required to get the cylinders to move without any flow obstruction.) The air pressure was then increased gradually until the valve could no longer hold back the MR pressure and the cylinders moved slowly. The maximum air pressure that could be held without movement of the cylinders was 85 psi; however. as much as 30 psi of this pressure may be required to overcome stiction. Thus, the maximum pressure we were able to stop was somewhere between 55 and 85 psi of air. This translates into 1500 to 2330 psi MR fluid pressure. Based on the ratio of the piston area to that of the MR damper valve, this in turn translates to a force of 9,700 to 15,000 pounds. A force of this magnitude is what is required for operation of the damper under typical downhole conditions. Initial testing indicates that a valve capable of producing the required damping under the anticipated downhole conditions is technically feasible. The project is progressing, but behind schedule, and a four-month extension of Phase I is being requested. This extension will not alter the budget for Phase I and is expected to have no significant effect upon the overall program schedule or budget.
Preventing Reverse Engineering Threat in Java Using Byte Code Obfuscation Techniques (2006)

Java programs are complied in to a platform independent byte code format. Much of the information contained in the source code is retained in the byte code. Consequently reverse engineering becomes much easier. Several software protection techniques have been developed, of which, code obfuscation seems to be a promising one. In this paper, two new byte code obfuscation techniques have been evolved. These techniques involve applying obfuscating transformations to the Java byte code. These techniques prevent automatic software analysis tools, de-compilers, from producing correct source code by introducing syntax and semantic errors in the generated source code. The proposed techniques are applied on sample Java class files to examine the effectiveness of the techniques in impeding reverse engineering. The results reveal the erroneous codes generated by the tested de-compilers
Cytoplasmic filaments and gap junctions in epithelial cells and myofibroblasts during wound healing. (1978)

During the healing of an experimental skin wound, epidermal cells and granulation tissue fibroblasts (myofibroblasts) develop an extensive cytoplasmic contactile apparatus. Concurrently, the proportion of epidermal cell surface occupied by gap junctions increases when compared to normal skin, and newly formed gap junctions appear between myofibroblasts; this suggests that epidermal cell migration and granulation tissue contraction are synchronized phenomena.
Effect of Shock Timing on Defibrillation Success (1997)

The goal of this study was to determine whether delivering transvenous defibrillation shocks, coordinated with the up/down-slope VF waveform patterns in the shocking lead, would improve the probability of successful defibrillation. Anesthetized swine (32-38 kg, n = 8) were implanted with an RV-->SVC + SQArray transvenous system to measure VF waveform patterns and to deliver shocks. The shocks were generated by a Cardiac Pacemakers Inc. biphasic waveform generator. Energy required for 50% success probability (E50) was determined using the multishock up-down protocol. VF was repeatedly induced and defibrillation shocks at E50 were given after 10 seconds. The defibrillation outcome, delivered energy (Ed), peak voltage (V), peak current (I), system impedance (Z) and VF waveform pattern at the time of shock were recorded and measured. Out of a total of 685 shocks, 324 (47%) succeeded and 361 (53%) failed. The Ed, V, I, and Z were similar for the two defibrillation outcome groups (success or failure). VF patterns were classified as high or low amplitude at the time of the shock based on the peak-to-peak amplitude of signals recorded between the shocking electrodes. Shocks that coincided with high amplitude VF patterns were further divided into shocks that occurred on the up-slope or on the down-slope. The probability of success when the E50 shocks were coincident with high or low amplitude fibrillation did not differ significantly (Student's t-test: 46% vs 48%. P = NS). However, during high amplitude fibrillation, shocks delivered on the up-slope were significantly more successful than those delivered on the down-slope (Chi-square: 67% vs 39%; P < 0.001). These results suggest that delivering defibrillation shocks during the up-slope of the high amplitude signal in the shocking lead may improve the probability of successful defibrillation of ICDs.
Multilevel converters for large electric drives (2002)

Traditional two-level high-frequency pulse width modulation (PWM) inverters for motor drives have several problems associated with their high frequency switching which produces common-mode voltage and high voltage change (dV/dt) rates to the motor windings. Multilevel inverters solve these problems because their devices can switch at a much lower frequency. Two different multilevel topologies are identified for use as a power converter for electric drives: a cascade inverter with separate DC sources; and a back-to-back diode clamped converter. The cascade inverter is a natural fit for large automotive all-electric drives because of the high VA ratings possible and because it uses several levels of DC voltage sources which would be available from batteries or fuel cells. The back-to-back diode clamped converter is ideal where a source of AC voltage is available such as a hybrid electric vehicle. Simulation and experimental results show the superiority of these two power converters over PWM-based drives.
Shape and volume change in the transtibial residuum over the short term: Preliminary investigation of six subjects (2004)

A preliminary investigation was conducted to characterize the magnitude and distribution of volume change in transtibial residua at two time intervals: upon prosthesis removal and at 2 week intervals. Six adult male unilateral transtibial amputee subjects, between 0.75 and 40.0 years since amputation, were imaged 10 times over a 35-minute interval with a custom residual limb optical scanner. Volume changes and shape changes over time were assessed. Measurements were repeated 2 weeks later. Volume increase on socket removal for the six subjects ranged from 2.4% to 10.9% (median 6.0% +/- standard deviation 3.6%). Rate of volume increase was highest immediately upon socket removal and decreased with time (five subjects). In four subjects, 95% of the volume increase was reached within 8 minutes. No consistent proximal-to-distal differences were detected in limb cross-sectional area change over time. Limb volume differences 2 weeks apart ranged from -2.0% to 12.6% (0.6% +/- 5.5%) and were less in magnitude than those within a session over the 35-minute interval (five subjects). Multiple mechanisms of fluid movement may be responsible for short-term volume changes, with different relative magnitudes and rates in different amputees.
Factors Influencing the Efficiency of Miscible Displacement (1959)

Published in Petroleum Transactions, AIME, Volume 217, 1959, pages 1–8. Abstract This paper presents results of an experimental investigation of factors that control the efficiency with which oil is displaced from porous media by a miscible fluid. The study was made to elucidate the relevant processes both on microscopic level (within individual or between neighboring pore spaces) and on macroscopic level (within a large sand body). Mixing of miscible fluids on the microscopic level was studied in sand-packed tubes. It was found that molecular diffusion is the dominant dispersion mechanism for reservoir conditions of rate, length and pore sizes. Macroscopic channeling was studied for various mobility ratios in reservoir models-scaled to relate viscous gravitational, and diffusional forces. The formation of channels was due to viscous fingering, gravity segregation and variations in permeability. With adverse mobility ratios, it was found for reservoirs of realistic widths that diffusion will not be effective in preventing the formation and growth of fingers, even in homogeneous sands. At sufficiently low rates channeling was eliminated by gravity segregation in tilted reservoirs. The dependence of recovery on mobility ratio, length-to-width ratio, flow rate and angle of dip is presented. Introduction Oil recovery by solvent flooding is finding increasing application in the field. while the process promises high recoveries from the region swept by solvent, under adverse conditions only a small fraction of the reservoir volume may be swept at the time solvent breaks through to the producing well. Further, the high cost of the solvent encourages its use only as a bank whose size must be kept at a minimum. Thus, two important questions arise:what fraction of the reservoir can be swept, practically, by solvent? andwhat is the minimum size solvent bank that can be used to carry out the displacement? The answers to these questions require knowledge of both macroscopic channeling processes and microscopic mixing processes. The studies described here were carried out to gain this knowledge. Microscopic mechanisms which cause mixing will be discussed first, because an understanding of these mechanisms is necessary for proper interpretation of the experimental work on channeling described later.
Human medial gastrocnemius force–velocity behavior shifts with locomotion speed and gait (2012)

Humans walk and run over a wide range of speeds with remarkable efficiency. For steady locomotion, moving at different speeds requires the muscle-tendon units of the leg to modulate the amount of mechanical power the limb absorbs and outputs in each step. How individual muscles adapt their behavior to modulate limb power output has been examined using computer simulation and animal models, but has not been studied in vivo in humans. In this study, we used a combination of ultrasound imaging and motion analysis to examine how medial gastrocnemius (MG) muscle-tendon unit behavior is adjusted to meet the varying mechanical demands of different locomotor speeds during walking and running in humans. The results highlighted key differences in MG fascicle-shortening velocity with both locomotor speed and gait. Fascicle-shortening velocity at the time of peak muscle force production increased with walking speed, impairing the ability of the muscle to produce high peak forces. Switching to a running gait at 2.0 m·s(-1) caused fascicle shortening at the time of peak force production to shift to much slower velocities. This velocity shift facilitated a large increase in peak muscle force and an increase in MG power output. MG fascicle velocity may be a key factor that limits the speeds humans choose to walk at, and may explain the transition from walking to running. This finding is consistent with previous modeling studies.
A new type of mutation in phytochrome A causes enhanced light sensitivity and alters the degradation and subcellular partitioning of the photoreceptor (2004)

A specific light program consisting of multiple treatments with alternating red and far-red light pulses was used to isolate mutants in phytochrome A-dependent signal transduction pathways in Arabidopsis. Because of their phenotype, the mutants were called eid for empfindlicher im dunkelroten Licht, which means hypersensitive in far-red light. One of the isolated mutants, eid4, is a novel semi-dominant allele of the phytochrome A gene that carries a missense mutation in the chromophore-binding domain. The mutation did not change the photochemical properties of the photoreceptor, but it leads to an increased stability under light conditions that induce its rapid degradation. Fusion proteins with the green fluorescent protein exhibited clear alterations in subcellular localization of the mutated photoreceptor: The fusion protein was impaired in the formation of sequestered areas of phytochrome in the cytosol, which can explain its reduced light-dependent degradation. In contrast, the mutation stabilizes nuclear speckles (NUS) that appear late under continuous far-red light, whereas the formation of early, transiently appearing NUS remained more or less unaltered.
Synthesis of 3,4,5-Trimethoxybenzaldehyde (1990)

Abstract The copper [I]-catalyzed exchange of bromine by methoxide in 5-bromovanillin and in 3,5-dibromo-4-hydroxybenzaldehyde provides an efficient method for preparing 3,5-dimethoxy-4-hydroxybenzaldehyde, from which 3,4,5-trimethoxybenzaldehyde is obtained by methylation with dimethylsulfate.