gebhart/patrepeval huggingface dataset:
Tumor targeting by covalent conjugation of a natural fatty acid to paclitaxel. (2001)

Certain natural fatty acids are taken up avidly by tumors for use as biochemical precursors and energy sources. We tested in mice the hypothesis that the conjugation of docosahexaenoic acid (DHA), a natural fatty acid, and an anticancer drug would create a new chemical entity that would target tumors and reduce toxicity to normal tissues. We synthesized DHA-paclitaxel, a 2'-O-acyl conjugate of the natural fatty acid DHA and paclitaxel. The data show that the conjugate possesses increased antitumor activity in mice when compared with paclitaxel. For example, paclitaxel at its optimum dose (20 mg/kg) caused neither complete nor partial regressions in any of 10 mice in a Madison 109 (M109) s.c. lung tumor model, whereas DHA-paclitaxel caused complete regressions that were sustained for 60 days in 4 of 10 mice at 60 mg/kg, 9 of 10 mice at 90 mg/kg, and 10 of 10 mice at the optimum dose of 120 mg/kg. The drug seems to be inactive as a cytotoxic agent until metabolized by cells to an active form. The conjugate is less toxic than paclitaxel, so that 4.4-fold higher molar doses can be delivered to mice. DHA-paclitaxel in rats has a 74-fold lower volume of distribution and a 94-fold lower clearance rate than paclitaxel, suggesting that the drug is primarily confined to the plasma compartment. DHA-paclitaxel is stable in plasma, and high concentrations are maintained in mouse plasma for long times. Tumor targeting of the conjugate was demonstrated by pharmacokinetic studies in M109 tumor-bearing mice, indicating an area under the drug concentration-time curve of DHA-paclitaxel in tumors that is 8-fold higher than paclitaxel at equimolar doses and 57-fold higher at equitoxic doses. At equimolar doses, the tumor area under the drug concentration-time curve of paclitaxel derived from i.v. DHA-paclitaxel is 6-fold higher than for paclitaxel derived from i.v. paclitaxel. Even at 2 weeks after treatment, 700 nM paclitaxel remains in the tumors after DHA-paclitaxel treatment. Low concentrations of DHA-paclitaxel or paclitaxel derived from DHA-paclitaxel accumulate in gastrocnemius muscle; which may be related to the finding that paclitaxel at 20 mg/kg caused hind limb paralysis in nude mice, whereas DHA-paclitaxel caused none, even at doses of 90 or 120 mg/kg. The dose-limiting toxicity in rats is myelosuppression, and, as in the mouse, little DHA-paclitaxel is converted to paclitaxel in plasma. Because DHA-paclitaxel remains in tumors for long times at high concentrations and is slowly converted to cytotoxic paclitaxel, DHA-paclitaxel may kill those slowly cycling or residual tumor cells that eventually come into cycle.
All-trans retinoic acid promotes neural lineage entry by pluripotent embryonic stem cells via multiple pathways (2009)

RA can promote neural lineage entry by ESCs in adherent monolayer culture systems. This effect depends on RA signaling and its crosstalk with the ERK and Wnt pathways.
Medullary Thyroid Carcinoma: Prognosis of FamilialVersusSporadic Disease and the Role of Radiotherapy* (1988)

A retrospective study of 202 patients with medullary thyroid carcinoma (MTC) diagnosed between 1943 and 1987 was done to compare the prognosis of patients with sporadic disease and those with the familial form of multiple endocrine neoplasia type II and to study the effect of radiotherapy. Patients with multiple endocrine neoplasia type II had a significantly higher survival rate than did patients with the sporadic variety (P less than 0.005), but most patients with sporadic tumors were older and had more advanced disease. No differences in survival rates were found when patients from these 2 groups were matched for age and involvement of the thyroid gland only (P greater than 0.3), involvement of the thyroid gland plus cervical nodes (P greater than 0.3), and involvement of the thyroid gland, cervical nodes, and soft tissue (P greater than 0.7). When patients with MTC who received radiotherapy were matched for age, extent of disease, and surgery with patients who had had no radiotherapy, the latter group was found to live significantly longer (P less than 0.05). We conclude that 1) the apparently poor prognosis of patients with the sporadic variety of MTC may be related to the patients' older age at detection rather than to inherent differences in the two forms of disease, and 2) radiotherapy has little effect on MTC.
The QRxGRxGRxxxG motif of the vaccinia virus DExH box RNA helicase NPH-II is required for ATP hydrolysis and RNA unwinding but not for RNA binding (1996)

Vaccinia virus NPH-II is an essential nucleic acid-dependent nucleoside triphosphate that catalyzes unidirectional unwinding of duplex RNA containing a 3' tail. NPH-II is the prototypal RNA helicase of the DExH box protein family, which is defined by several shared sequence motifs. The contribution of the conserved QRKGRVGRVNPG region to enzyme activity was assessed by alanine-scanning mutagenesis. Ten mutated versions of NPH-II were expressed in vaccinia virus-infected BSC-40 cells and purified by nickel affinity chromatography and glycerol gradient sedimentation. The mutated proteins were characterized with respect to RNA helicase, nucleic acid-dependent ATPase, and RNA binding functions. Individual alanine substitutions at invariant residues Q-491, G-494, R-495, G-497, R-498, and G-502 caused severe defects in RNA unwinding that correlated with reduced rates of ATP hydrolysis. None of these mutations affected the binding of NPH-II to single-strand RNA or to the tailed duplex RNA used as a helicase substrate. Mutation of the strictly conserved position R-492 inhibited ATPase and helicase activities and also caused a modest decrement in RNA binding. Alanine mutations at the nonconserved position N-500 and the weakly conserved residue P-501 had no apparent effect on any activity associated with NPH-II, whereas a mutation at the weakly conserved position K-493 reduced helicase to one-third and ATPase to two-thirds of the activity of wild-type required for ATP hydrolysis and RNA unwinding but not for RNA binding. Because mutations in the HRxGRxxR motif of the prototypal DEAD box RNA helicase eIF-4A abolish or severely inhibit RNA binding, we surmise that the contribution of conserved helicase motifs to overall protein function is context dependent.
Identification of a Rough Strain of Escherichia coli O157:H7 That Produces No Detectable O157 Antigen (1998)

MA6, an O157:H7-like strain, did not react with most anti-O157 kits examined; however, it had the rfbE gene that is essential for O157 expression and carried O157:H7 virulence factors. Lipopolysaccharide analysis showed that MA6 is a rough strain that does not produce the O157 antigen, but genetically, it belongs in the O157:H7 clonal group.
Functional properties of proximal tubule cell lines derived from transgenic mice harboring L-pyruvate kinase-SV40 (T) antigen hybrid gene (1993)

This study describes the functional characterization of two cell lines derived from the proximal convoluted (PKSV-PCT cells) and proximal straight (PKSV-PR) tubules microdissected out from kidneys of transgenic mice harboring the simian virus 40 (SV40) large T and small t antigens placed under the control of the rat L-type pyruvate kinase (L-PK) 5' regulatory sequence. Both cell lines exhibited cellular cyclic AMP stimulated by parathormone (PTH) and calcitonin (CT) and a sodium-dependent glucose transporter. Uptake of the fluid-phase marker [3H]inulin showed that both cell lines grown on filters exhibited biphasic apical and basolateral endocytic rates. Results from Northern blot analysis indicate that the expression of the T antigen gene (Tag) is dependent on the concentration of D-glucose in the medium and show that the L-PK construct has maintained its capacity for up- or down-regulation by carbohydrates. Replacement of D-glucose by neoglucogenic substrates (lactate, oxaloacetate) blunted the expression of Tag transcripts and induced arrest of cell growth. Compared to cell grown in D-glucose-enriched medium, the hormonal sensitivities to PTH and CT and the sodium-dependent glucose uptake were unchanged whereas quiescent cells exhibited increased hydrolase content. Thus the proximal function has been preserved in these cultured cells derived from tissue-specific targeted oncogenesis in transgenic mice. As the expression of Tag transcripts is controlled by D-glucose, the structural and physiological characteristics of these cell lines can be studied in either quiescent or active growth conditions.
Blue semiconductor nanocrystal laser (2005)

We demonstrate tunable room-temperature amplified spontaneous emission and lasing from blue-emitting core-shell CdS∕ZnS nanocrystals (NCs) stabilized in a sol-gel derived silica matrix. Variable stripe length measurements show that these NC-silica composites have a modal gain of ∼100cm−1 at room temperature. Coating microspheres with a NC-silica composite film via a facile process resulted in uniform resonators that exhibit room-temperature lasing over long periods of continuous excitation. This work opens up a spectral window for emission tunable, microscale NC-based lasers.
Quantitative Comparison of Photoplethysmographic Waveform Characteristics: Effect of Measurement Site (2019)

<b>Introduction:</b> Photoplethysmography (PPG) has been widely used to assess cardiovascular function. However, few studies have comprehensively investigated the effect of measurement site on PPG waveform characteristics. This study aimed to provide a quantitative comparison on this. <b>Methods:</b> Thirty six healthy subjects participated in this study. For each subject, PPG signals were sequentially recorded for 1 min from six different body sites (finger, wrist under (anatomically volar), wrist upper (dorsal), arm, earlobe, and forehead) under both normal and deep breathing patterns. For each body site under a certain breathing pattern, the mean amplitude was firstly derived from recorded PPG waveform which was then normalized to derive several waveform characteristics including the pulse peak time (Tp), dicrotic notch time (Tn), and the reflection index (RI). The effects of breathing pattern and measurement site on the waveform characteristics were finally investigated by the analysis of variance (ANOVA) with <i>post hoc</i> multiple comparisons. <b>Results:</b> Under both breathing patterns, the PPG measurements from the finger achieved the highest percentage of analyzable waveforms for extracting waveform characteristics. There were significant effects of breathing pattern on Tn and RI (larger Tn and smaller RI with deep breathing on average, both <i>p</i> < 0.03). The effects of measurement site on mean amplitude, Tp, Tn, and RI were significant (all <i>p</i> < 0.001). The key results were that, under both breathing patterns, the mean amplitude from finger PPG was significantly larger and its Tp and RI were significantly smaller than those from the other five sites (all <i>p</i> < 0.001, except <i>p</i> = 0.04 for the Tp of "wrist under"), and Tn was only significantly larger than that from the earlobe (both <i>p</i> < 0.05). <b>Conclusion:</b> This study has quantitatively confirmed the effect of PPG measurement site on PPG waveform characteristics (including mean amplitude, Tp, Tn, and RI), providing scientific evidence for a better understanding of the PPG waveform variations between different body sites.
Phenylalanine Ammonia-Lyase: The Use of Its Broad Substrate Specificity for Mechanistic Investigations and Biocatalysis—Synthesis ofL-Arylalanines (2000)

Several fluoro- and chlorophenylalanines were found to be good substrates of phenylalanine ammonia-lyase (PAL/EC 4.3.1.5) from parsley. The enantiomerically pure L-amino acids were obtained in good yields by reaction of the corresponding cinnamic acids with 5M ammonia solution (buffered to pH 10) in the presence of PAL. The kinetic constants for nine different fluoro- and chlorophenylalanines do not provide a rigorous proof for but are consistent with the previously proposed mechanism comprising an electrophilic attack of the methylidene-imidazolone cofactor of PAL at the aromatic nucleus as a first chemical step. In the resulting Friedel-Crafts-type sigma complex the beta-protons are activated for abstraction and consequently the pro-S is abstracted by an enzymic base. Results from semi-empirical calculations combined with a proposed partial active site model showed a correlation between the experimental kinetic constants and the change in polarization of the pro-S Cbeta-H bond and heat of formation of the sigma complexes, thus making the electrophilic attack at the neutral aromatic ring plausible. Furthermore, while 5-pyrimidinylalanine was found to be a moderately good substrate of PAL, 2-pyrimidinylalanine was an inhibitor.
Specific tolerance to an acetylcholine receptor epitope induced in vitro in myasthenia gravis CD4+ lymphocytes by soluble major histocompatibility complex class II-peptide complexes. (1994)

In autoimmune disorders, inactivation of pathogenic antigen-specific T cells, rather than global immunosuppression, would be highly desirable. One way to achieve this would be to deliver the first antigen-specific signal to the T cell in the absence of the second costimulatory signal. Myasthenia gravis (MG) is a well-characterized autoimmune disease in which T cell-dependent autoantibodies are directed against the acetylcholine receptor (A ChR) at the neuromuscular junction. AChR-specific T cells have been cloned from MG patients, and in this study, we have induced long-lasting tolerance in vitro in one particular clone (PM-A1) with a known peptide epitope (alpha 144-163) and MHC class II restriction (DR4 Dw14.2 or 4.2) by using soluble MHC-class II peptide complexes. Preincubation of PM-A1 T cells with such complexes induced death by apoptosis in < or = 40-50% of the AChR-specific cells. Surviving cells remained refractory to stimulation with AChR-derived synthetic peptides or recombinant polypeptides for < or = 38 d after complex treatment. These effects were highly specific, dose-dependent and required > 2 h preincubation. The T cells could be protected from the tolerizing effects of complex by coincubation with DR-matched or -mismatched antigen-presenting cells. This work shows that antigen-specific T cells can be selectively killed or anergized using soluble MHC class II: peptide complexes. Such an antigen-specific therapy offers a rational approach to the immunotherapy of autoimmune or allergic disease in vivo.
Modification of Activity and Specificity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26 by Engineering of Its Entrance Tunnel (2003)

Structural comparison of three different haloalkane dehalogenases suggested that substrate specificity of these bacterial enzymes could be significantly influenced by the size and shape of their entrance tunnels. The surface residue leucine 177 positioned at the tunnel opening of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 was selected for modification based on structural and phylogenetic analysis; the residue partially blocks the entrance tunnel, and it is the most variable pocket residue in haloalkane dehalogenase-like proteins with nine substitutions in 14 proteins. Mutant genes coding for proteins carrying all possible substitutions in position 177 were constructed by site-directed mutagenesis and heterologously expressed in Escherichia coli. In total, 15 active protein variants were obtained, suggesting a relatively high tolerance of the site for the introduction of mutations. Purified protein variants were kinetically characterized by determination of specific activities with 12 halogenated substrates and steady-state kinetic parameters with two substrates. The effect of mutation on the enzyme activities varied dramatically with the structure of the substrates, suggesting that extrapolation of one substrate to another may be misleading and that a systematic characterization of the protein variants with a number of substrates is essential. Multivariate analysis of activity data revealed that catalytic activity of mutant enzymes generally increased with the introduction of small and nonpolar amino acid in position 177. This result is consistent with the phylogenetic analysis showing that glycine and alanine are the most commonly occurring amino acids in this position among haloalkane dehalogenases. The study demonstrates the advantages of using rational engineering to develop enzymes with modified catalytic properties and substrate specificities. The strategy of using site-directed mutagenesis to modify a specific entrance tunnel residue identified by structural and phylogenetic analyses, rather than combinatorial screening, generated a high percentage of viable mutants.
In vivo discovery of a peptide that prevents CUG–RNA hairpin formation and reverses RNA toxicity in myotonic dystrophy models (2011)

Myotonic dystrophy type 1 (DM1) is caused by the expansion of noncoding CTG repeats in the dystrophia myotonica-protein kinase gene. Mutant transcripts form CUG hairpins that sequester RNA-binding factors into nuclear foci, including Muscleblind-like-1 protein (MBNL1), which regulate alternative splicing and gene expression. To identify molecules that target toxic CUG transcripts in vivo, we performed a positional scanning combinatorial peptide library screen using a Drosophila model of DM1. The screen identified a D-amino acid hexapeptide (ABP1) that reduced CUG foci formation and suppressed CUG-induced lethality and muscle degeneration when administered orally. Transgenic expression of natural, L-amino acid ABP1 analogues reduced CUG-induced toxicity in fly eyes and muscles. Furthermore, ABP1 reversed muscle histopathology and splicing misregulation of MBNL1 targets in DM1 model mice. In vitro, ABP1 bound to CUG hairpins and induced a switch to a single-stranded conformation. Our findings demonstrate that ABP1 shows antimyotonic dystrophy activity by targeting the core of CUG toxicity.
[Studies on flavonoids of Oxytropis falcata]. (2007)

All compounds were obtained from O. falcata for the first time.
Cardiac Allograft Vasculopathy and Dysregulation of the NO Synthase Pathway (2003)

Cardiac allograft vasculopathy is the most aggressive form of atherosclerosis in humans and is the leading cause of death after the first year of heart transplantation. Endothelial dysfunction is a major contributing factor to the acceleration of coronary vascular disease in these individuals. A reflection of this endothelial dysfunction is the severe impairment in endothelium-dependent vasodilation that occurs early after transplantation. The etiology of this allograft endothelial alteration is multifactorial and may include preexisting atherosclerosis of the graft vessels, reperfusion injury during transplantation, denervation, disruption of the lymphatic system, and acute and chronic immune injury, as well as traditional risk factors for coronary artery disease (hyperlipidemia, diabetes, hypertension, or hyperhomocysteinemia) and pathogens, such as cytomegalovirus. The alteration in endothelial function affects vasomotor tone of the coronary arteries. Evidence indicates that there may be an impairment of endothelial production and/or activity of NO. Because NO is a potent vasodilator, its deficiency would explain the abnormal vasomotor tone in these individuals. In addition, because NO inhibits key processes in vascular inflammation and atherosclerosis, its absence may contribute to the acceleration of transplant vascular disease. Recent studies from our group and others have shed light on the mechanisms of endothelial dysfunction and its importance in cardiac allograft vasculopathy. In addition, the alteration in endothelial function contributes to vascular inflammation and progression of the disease.
Servicer performance in processing HAMP loan modifications: a survey of Massachusetts-based counseling agencies (2011)

The Home Affordable Mortgage Program (HAMP) attempts to help homeowners avoid foreclosure by compensating servicers that allow borrowers to modify the terms of their mortgages. To understand the seemingly troubled HAMP process, the Community Development unit of the Boston Federal Reserve Bank of Boston administered surveys to loan-modification counselors. The results indicate that the process takes much longer than the guidelines indicate and that servicers frequently claim the applications are incomplete. The surveys were run twice to assess any improvements.
A Supercapacitor-Based Energy Storage Substation for Voltage Compensation in Weak Transportation Networks (2004)

A supercapacitive-storage-based substation for the compensation of resistive voltage drops in transportation networks is proposed. It allows to feed as a current source in any voltage conditions of the line. The system has been designed as a compensation substation to be placed at weak points like end-of-line stations, instead of additional feeding substations. A dedicated power-electronic converter with an associated control system for the stabilization of the voltage level at the point of coupling in case of strong perturbations is proposed. Practical results are also presented, which have been recorded from a reduced size prototype.
Gas Separation by Adsorption in Order to Increase CO2 Conversion to CO via Reverse Water Gas Shift (RWGS) Reaction (2013)

In this research project, adsorption is considered in conjunction with the reverse water gas shift reaction in order to convert CO2 to CO for synthetic fuel production. If the CO2 for this process can be captured from high emitting industries it can be a very good alternative for reduced fossil fuel consumption and GHG emission mitigation. CO as an active gas could be used in Fischer-Tropsch process to produce conventional fuels. Literature review and process simulation were carried out in order to determine the best operating conditions for reverse water gas shift (RWGS) reaction. Increasing CO2 conversion to CO requires CO2/CO separation downstream of the reactor and recycling unreacted CO2 and H2 back into the reactor. Adsorption as a viable and cost effective process for gas separation was chosen for the CO2/CO separation. This was started by a series of adsorbent screening experiments to select the best adsorbent for the application. Screening study was performed by comparing pure gas isotherms for CO2 and CO at different temperatures and pressures. Then experimental isotherm data were modeled by the Temperature-Dependent Toth isotherm model which provided satisfactory fits for these isotherms. Henry law’s constant, isosteric heat of adsorption and binary mixture prediction were determined as well as selectivity for each adsorbent. Finally, the expected working capacity was calculated in order to find the best candidate in terms of adsorption and desorption. Zeolite NaY was selected as the best candidate for CO2/CO separation in adsorption process for this project. In the last step breakthrough experiments were performed to evaluate operating condition and adsorption capacity for real multi component mixture of CO2, CO, H2 in both cases of saturated with water and dry gas basis. In multi components experiments zeolite NaY has shown very good performance to separate CO2/CO at low adsorption pressure and ambient temperature. Also desorption experiment was carried out in order to evaluate the working capacity of the adsorbent for using in industrial scale and eventually temperature swing adsorption (TSA) process worked very well for the regeneration step. Integrated adsorption system downstream of RWGS reactor can enhance the conversion of CO2 to CO in this process significantly resulting to provide synthetic gas for synthetic fuel production as well as GHG emission mitigation.