gebhart/patrepeval huggingface dataset:
Abietadiene Synthase from Grand Fir (Abies grandis):  Characterization and Mechanism of Action of the “Pseudomature” Recombinant Enzyme (2000)

The oleoresin secreted by grand fir (Abies grandis) is composed of resin acids derived largely from the abietane family of diterpene olefins as precursors which undergo subsequent oxidation of the C18-methyl group to a carboxyl function, for example, in the conversion of abieta-7,13-diene to abietic acid. A cDNA encoding abietadiene synthase has been isolated from grand fir and the heterologously expressed bifunctional enzyme shown to catalyze both the protonation-initiated cyclization of geranylgeranyl diphosphate to the intermediate (+)-copalyl diphosphate and the ionization-dependent cyclization of (+)-copalyl diphosphate, via a pimarenyl intermediate, to the olefin end products. Abietadiene synthase is translated as a preprotein bearing an N-terminal plastidial targeting sequence, and this form of the recombinant protein expressed in Escherichia coli proved to be unsuitable for detailed structure-function studies. Since the transit peptide-mature protein cleavage site could not be determined directly, a truncation series was constructed to delete the targeting sequence and prepare a "pseudomature" form of the enzyme that resembled the native abietadiene synthase in kinetic properties. Both the native synthase and the pseudomature synthase having 84 residues deleted from the preprotein converted geranylgeranyl diphosphate and the intermediate (+)-copalyl diphosphate to a nearly equal mixture of abietadiene, levopimaradiene, and neoabietadiene, as well as to three minor products, indicating that this single enzyme accounts for production of all of the resin acid precursors of grand fir. Kinetic evaluation of abietadiene synthase with geranylgeranyl diphosphate and (+)-copalyl diphosphate provided evidence for two functionally distinct active sites, the first for the cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate and the second for the cyclization of (+)-copalyl diphosphate to diterpene end products, and demonstrated that the rate-limiting step of the coupled reaction sequence resides in the second cyclization process. The structural implications of these findings are discussed in the context of primary sequence elements considered to be responsible for binding the substrate and intermediate and for initiating the respective cyclization steps.
ATP-Sensitive Potassium (KATP) Channel Activation Decreases Intraocular Pressure in the Anterior Chamber of the Eye (2011)

PURPOSE. ATP-sensitive potassium channel (K(ATP)) openers target key cellular events, many of which have been implicated in glaucoma. The authors sought to determine whether K(ATP) channel openers influence outflow facility in human anterior segment culture and intraocular pressure (IOP) in vivo. METHODS. Anterior segments from human eyes were placed in perfusion organ culture and treated with the K(ATP) channel openers diazoxide, nicorandil, and P1075 or the K(ATP) channel closer glyburide (glibenclamide). The presence, functionality, and specificity of K(ATP) channels were determined by RT-PCR, immunohistochemistry, and inside-out patch clamp in human trabecular meshwork (TM) tissue or primary cultures of normal human trabecular meshwork (NTM) cells. The effect of diazoxide on IOP in anesthetized Brown Norway rats was measured with a rebound tonometer. RESULTS. K(ATP) channel openers increased outflow facility in human anterior segments (0.14 ± 0.02 to 0.26 ± 0.09 μL/min/mm Hg; P < 0.001) compared with fellow control eyes (0.22 ± 0.11 to 0.21 ± 0.11 μL/min/mm Hg; P > 0.5). The effect was reversible, with outflow facility returning to baseline after drug removal. The addition of glyburide inhibited diazoxide from increasing outflow facility. Electrophysiology confirmed the presence and specificity of functional K(ATP) channels. K(ATP) channel subunits K(ir)6.1, K(ir)6.2, SUR2A, and SUR2B were expressed in TM and NTM cells. In vivo, diazoxide significantly lowered IOP in Brown Norway rats. CONCLUSIONS. Functional K(ATP) channels are present in the trabecular meshwork. When activated by K(ATP) channel openers, these channels increase outflow facility through the trabecular outflow pathway in human anterior segment organ culture and decrease IOP in Brown Norway rat eyes.
Studies Comparing Kollicoat MAE 30 D with Commercial Cellulose Derivatives for Enteric Coating on Caffeine Cores (1998)

The products that are processed in aqueous form, such as Aqoat MF (suspension), Aquateric (pseudolatex), HP 55 (ammonia-based solution), and Kollicoat MAE 30 D (latex), were compared (in the form of spray dispersions, isolated films prepared from the dispersions, and caffeine-film-coated tablets with 5.5, 8.0, and 11.0 mg film/cm2) with one another and with ethanolic HP 55 S solution. The addition of pigments to all of the liquid preparations, with the exception of the ammoniacal solution of HP 55, led to a slight increase in pH. In each case, the viscosity of both solutions was well above that of the other formulations. The minimum film-forming temperature was decidedly reduced by the addition of pigment. Kollicoat MAE was the undissolved film-former that had the smallest particle size and particle size distribution. The next smallest were those of Aqoat MF. The latex and the suspension were the only products that were sensitive to shear and heat. The isolated films did not display any tack. The strongest films and the films most impermeable to water vapor were obtained from solutions, and this can be ascribed to the fine distribution of the film-former. None of the isolated films showed signs of dissolving at pH 4.5. At pH 5.5, only the HP 55 was dissolved. This was because HP 55 was processed in ammonia-based solution; as a result of which, films that were not very resistant to gastric juice were obtained. The other formulations did not dissolve until the pH reached 6.0. As the pH rose, the rate of dissolution increased for all of the films. The permeability to protons was similar to that of caffeine-film-coated tablets to gastric juice. The resistance increased in the following sequence: HP 55 (ammonia-based) < Aquateric < Aqoat MF < HP 55 S (organic) and Kollicoat MAE. As a result of the temperature treatment and the rate of spraying, the production time on a 5-kg scale was twice as long for 5.5 mg Aqoat MF/cm2 as it was for Kollicoat MAE. This amount of film sufficed for Kollicoat MAE and HP 55 S solution to achieve adequate resistance to gastric juice. Aqoat MF did not attain the same resistance until a thickness of 11 mg film/cm2 was reached. Film tablets with Aquateric and ammonia-based HP 55 solution absorbed more than 20% of gastric juice at this film thickness.
An Integrated Flow Cytometry-Based System for Real-Time, High Sensitivity Bacterial Detection and Identification (2014)

Foodborne illnesses occur in both industrialized and developing countries, and may be increasing due to rapidly evolving food production practices. Yet some primary tools used to assess food safety are decades, if not centuries, old. To improve the time to result for food safety assessment a sensitive flow cytometer based system to detect microbial contamination was developed. By eliminating background fluorescence and improving signal to noise the assays accurately measure bacterial load or specifically identify pathogens. These assays provide results in minutes or, if sensitivity to one cell in a complex matrix is required, after several hours enrichment. Conventional assessments of food safety require 48 to 56 hours. The assays described within are linear over 5 orders of magnitude with results identical to culture plates, and report live and dead microorganisms. This system offers a powerful approach to real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection.
Synthesis of 2-[18F]Fluoroestradiol, a Potential Diagnostic Imaging Agent for Breast Cancer:  Strategies to Achieve Nucleophilic Substitution of an Electron-Rich Aromatic Ring with [18F]F- (1998)

To improve the pharmacokinetics of fluorine-18 labeled estrogens to be used as receptor-based imaging agents for the identification and staging of estrogen-receptor-positive breast carcinoma, we wanted to synthesize 2-[(18)F]fluoroestradiol. This compound has high affinity for the estrogen receptor and also binds very well to sex hormone binding globulin, a protein thought to protect estrogens from metabolism and deliver them to target tissues. We anticipated that this compound might have increased tumor uptake and reduced uptake in the liver. The synthesis of a [(18)F]fluoroaryl estrogen at the high specific activity, no-carrier-added level requires the use of [(18)F]F(-) as a precursor. Several strategies were explored for the synthesis of a [(18)F]fluoroaryl estrogen. The synthesis of 2-[(18)F]fluoroestradiol was eventually achieved by [(18)F]fluoride ion displacement of a trimethylammonium leaving group at C-2 of an estrogen, with additional activation being provided by a 6-keto group which was subsequently removed by reduction. Incorporation yields of fluorine-18 were between 20% and 50%. The potential of this new radiopharmaceutical as an imaging agent is being evaluated in an appropriate animal model.
Characterization of the aluminum and beryllium fluoride species which activate transducin. Analysis of the binding and dissociation kinetics. (1992)

Aluminofluoride and beryllofluoride complexes can activate the heterotrimeric G-proteins by binding next to GDP in the nucleotide site of their G alpha subunit and acting as analogs of the gamma-phosphate of a GTP. However, the exact structures of the activatory complexes in solution as well as those of the bound complexes in the nucleotide site are still disputed. We have studied, by monitoring the activation-dependent tryptophan fluorescence of transducin T alpha subunit, the pF (-log[F-]) and pH dependencies of the kinetics of activation and deactivation of T alpha GDP in the presence of NaF and aluminum or beryllium salts. Comparisons were made with the calculated pF and pH dependencies of the distribution of the metallofluoride complexes, in order to identify the activating species. We observed that the contribution of a magnesium-dependent mechanism of activation by fluoride (Antonny, B., Bigay, J., and Chabre, M. (1990) FEBS Lett. 268, 277-280) and effects due to slow equilibration kinetics between various aluminofluoride complexes could give rise to puzzling kinetics that had caused misinterpretations of previous results. Once corrected for these effects, our results suggest that with aluminum AlF3(OH)- is, rather than AlF4-, the main activating species and that the bound form of the complex is tetracoordinated GDP-AlF3. Deactivation kinetics depend on the free fluoride concentration in the medium, suggesting that the simple bimolecular scheme: T alpha GDP-AlF3 in equilibrium with T alpha GDP+AlF3(OH) does not fully describe the interaction. Fluorides in the bound complexes can also exchange with free F- ions in solution. With beryllium, two complexes are activatory: BeF3-.H2O and BeF2(OH)-.H2O. In the nucleotide site these give two tetracoordinated complexes, GDP.BeF3 and GDP.BeF2(OH), as shown by their different dissociation rates.
Comparative Effectiveness of Two Walking Interventions on Participation, Step Counts, and Health (2016)

An enhanced walking program significantly increases participation rates and daily step counts, which were associated with weight loss and reductions in body mass index.
Comparison of two chemical cleavage methods for preparation of a truncated form of recombinant human insulin-like growth factor I from a secreted fusion protein. (1989)

We have produced a naturally occurring variant of human insulin-like growth factor I, truncated by three amino acids at the amino terminus. The polypeptide is obtained as a fusion protein in Escherichia coli. The fusion partner is a synthetic IgG-binding peptide. During fermentation the fusion protein is secreted into the medium, and is purified on IgG--Sepharose prior to cleavage. Two different genes for the fusion protein were used, allowing chemical cleavage at either a tryptophan linker or a methionine linker between the fusion partner and the growth factor, using N-chlorosuccinimide (NCS) or cyanogen bromide (CNBr) respectively. A partial CNBr cleavage yielded the native peptide, whereas the NCS cleavage yielded a product in which the single methionine had been oxidized to the sulfoxide. The forms from both cleavage methods exhibited biological activity and were characterized after purification to homogeneity. Both cleavage methods gave products having correct N- and C-terminal ends. The purified product had a biological activity equal to that of corresponding material from natural sources, 15 000 U/mg. Modified forms of truncated IGF-I were also identified, purified and characterized. Modifications such as proteolysis and misincorporation of norleucine for methionine occurred during biosynthesis, while oxidation of methionine took place during both fermentation and chemical cleavage.
How to outwit the enemy: dendritic cells face Salmonella (2006)

Salmonella enterica serovar Typhi causes typhoid fever, a serious life-threatening systemic infection. In mice, a similar disease is caused by Salmonella enterica serovar Typhimurium. During typhoid fever, soon after attachment to the mucosal surface of the gut, bacteria come into contact with the dendritic cells (DCs). The ability to sample antigens, process and present them to naïve and mature T cells, in the context of major histocompatibility complex molecules, makes DCs indispensable for mounting a specific and efficient immune response to invading pathogens. These bacteria, however, have evolved a number of mechanisms to interfere with or subvert DC functions. This review aims to describe how Salmonella clashes with dendritic cells at different stages of infection as well as the war strategies of these two opposing sides.
Increased Tau Phosphorylation and Aggregation in the Hippocampus of Mice Overexpressing Corticotropin-Releasing Factor (2014)

Clinical and basic science research suggests that stress and/or changes in central stress signaling intermediates may be involved in Alzheimer's disease (AD) pathogenesis. Although the links between stress and AD remain unsettled, data from our group and others have established that stress exposure in rodents may confer susceptibility to AD pathology by inducing hippocampal tau phosphorylation (tau-P). Work in our laboratory has shown that stress-induced tau-P requires activation of the type-1 corticotropin-releasing factor receptor (CRFR1). CRF overexpressing (CRF-OE) mice are a model of chronic stress that display cognitive impairment at 9-10 month of age. In this study we used 6-7 month old CRF-OE mice to examine whether sustained exposure to CRF and stress steroids would impact hippocampal tau-P and kinase activity in the presence or absence of the CRFR1-specific antagonist, R121919, given daily for 30 days. CRF-OE mice had significantly elevated tau-P compared to wild type (WT) mice at the AT8 (S202/T204), PHF-1 (S396/404), S262, and S422 sites. Treating CRF-OE mice with R121919 blocked phosphorylation at the AT8 (S202/T204) and PHF-1 (S396/404) sites, but not at the S262 and S422 sites and reduced phosphorylation of c-Jun N Terminal Kinase (JNK). Examination of hippocampal extracts from CRF-OE mice at the ultrastructural level revealed negatively stained round/globular aggregates that were positively labeled by PHF-1. These data suggest critical roles for CRF and CRFR1 in tau-P and aggregation and may have implications for the development of AD cognitive decline.
TIM‐3 as a therapeutic target for malignant stem cells in acute myelogenous leukemia (2012)

Acute myeloid leukemia (AML) originates from self-renewing leukemic stem cells (LSCs), an ultimate therapeutic target for AML. Recent studies have shown that many AML LSC-specific surface antigens could be such candidates. T cell immunoglobulin mucin-3 (TIM-3) is expressed on LSCs in most types of AML, except for acute promyelocytic leukemia, but not on normal hematopoietic stem cells (HSCs). In mouse models reconstituted with human AML LSCs or human hematopoietic stem cells, a human TIM-3 mouse IgG2a antibody with complement-dependent and antibody-dependent cellular cytotoxic activities eradicates AML LSCs in vivo but does not affect normal human hematopoiesis. Thus, TIM-3 is one of the promising targets to eradicate AML LSCs.
Experimental Determination and Modeling of Bubble Size Distributions in Bubble Columns (1998)

Using a five point conductivity technique local values of bubble size, bubble velocity and gas fraction have been experimentally determined in a 288 mmID and 4.3 m high bubble column as a function of axial and radial position for the air/water and CO2/N2/aqueous MDEA systems. The experimental results are compared with predictions from a fundamental two-fluid model. The implementation of a non-steady lateral drag term in the two-fluid model has been shown. In addition to improving the physical realism of the model, it is found to give slight improvements in the predictions of the distributions of local bubble size. Predictions of bubble size are found in reasonable agreement with experimental values in the heterogeous flow regime, whereas they are still found to be unreliable at low gas velocities. Local void predictions are found in reasonable agreement with experimental values, but deviations occur in the homogeneous flow regime towards the wall. This is attributed to deficiencies in the simplified bubble size model, suggesting improvements of that . It is shown how the Sauter mean diameter as a measure for bubble size is a more sensitive parameter to the radial bubble structure variations in a bubble column than the number averaged diameter. An equation for the calculation of local volumetric gas flow rates, based on conductivity probe data, has been developed and is shown to give improved predictions compared to previous methods in the heterogeneous regime.
Modulation of the rat suprachiasmatic circadian clock by melatonin in vitro (1995)

The pineal hormone melatonin regulates daily and seasonal rhythms, at least in part through an action on the mammalian biological clock in the suprachiasmatic nuclei (SCN). Melatonin was tested in vitro (10(-15)-10(-6) M; ZT9.5-10.5) for its effect on the circadian peak in neuronal firing rate in the rat SCN slice. It produced a concentration-related phase advance (maximum advance = 3 +/- 0.3 h at 10(-9) M, n = 3; minimum effective concentration = 10(-13) M; EC50 = 1.2 x 10(-12) M). The melatonin receptor antagonist luzindole (10(-5) M) blocked the phase-advance produced by melatonin (10(-9) M), whilst having no effect on its own. These data show that the effect of melatonin on the SCN clock, measured via the circadian rhythm of neuronal firing rate in the nuclei, is consistent with a concentration-dependent action via a high affinity melatonin receptor.
Transfusion-associated (T-A)-AIDS in the United States. (1993)

To the end of December 1991, 4,709 persons with transfusion-associated (T-A)-AIDS were reported to the Centers for Disease Control and Prevention (CDC) (2.3% of 206,392 adult AIDS cases). Since 1990, the rate of T-A-AIDS case reporting has remained relatively constant at 160-190 cases diagnosed per quarter year. In comparison with other adults with AIDS, those with T-A-AIDS were more likely to be diagnosed with Candida esophagitis and wasting syndrome. Adults with T-A-AIDS tend to be older at diagnosis (mean age 55 years vs. 35 years), white (69% vs. 54%), and female (38% vs. 10%) than other adults with AIDS. However, these demographic differences have decreased over time. The median observed incubation period for T-A-AIDS was 58 months (range 1-154 mo.). Younger adult transfusion recipients had longer incubation periods than older adults. The changing epidemiology of T-A-AIDS reflects, in large part, the effectiveness of prevention strategies.
Searching for IRES (2006)

The cell has many ways to regulate the production of proteins. One mechanism is through the changes to the machinery of translation initiation. These alterations favor the translation of one subset of mRNAs over another. It was first shown that internal ribosome entry sites (IRESes) within viral RNA genomes allowed the production of viral proteins more efficiently than most of the host proteins. The RNA secondary structure of viral IRESes has sometimes been conserved between viral species even though the primary sequences differ. These structures are important for IRES function, but no similar structure conservation has yet to be shown in cellular IRES. With the advances in mathematical modeling and computational approaches to complex biological problems, is there a way to predict an IRES in a data set of unknown sequences? This review examines what is known about cellular IRES structures, as well as the data sets and tools available to examine this question. We find that the lengths, number of upstream AUGs, and %GC content of 5'-UTRs of the human transcriptome have a similar distribution to those of published IRES-containing UTRs. Although the UTRs containing IRESes are on the average longer, almost half of all 5'-UTRs are long enough to contain an IRES. Examination of the available RNA structure prediction software and RNA motif searching programs indicates that while these programs are useful tools to fine tune the empirically determined RNA secondary structure, the accuracy of de novo secondary structure prediction of large RNA molecules and subsequent identification of new IRES elements by computational approaches, is still not possible.
Ideal Bend Contour Trajectories for Single-Mode Operation of Low-Loss Overmoded Waveguides (2007)

Bend designs for single-mode operation of low-loss overmoded waveguides are presented. A class of contour trajectories for minimum radiation loss is derived analytically, and numerical optimization is used to find ideal trajectory parameters. Three-dimensional finite-difference time-domain simulations predict bend losses below 0.1 dB for 180deg-bends of overmoded silicon-on-insulator waveguides with a radius of R=1.5 mum. These findings are supported experimentally
Nucleoprotein of influenza A virus is a major target of immunodominant CD8+ T‐cell responses (2013)

Influenza A virus causes annual epidemics and sporadic pandemics, resulting in significant morbidity and mortality worldwide. Vaccines are currently available; however, they induce a non-strain-cross protective humoral immune response directed against the rapidly mutating surface glycoproteins, and thus need to be updated annually. As T cells are directed against more conserved internal influenza proteins, a T-cell-based vaccine has the potential to induce long-lasting and cross-strain protective CD8(+) T-cell immunity, and in that way minimize the severity of influenza infection. However, to rationally design such vaccines, we need to identify immunogenic T-cell regions within the most antigenic viral proteins. In this study, we have used a systematic approach to identify immunodominant peptides in HLA-A2-negative donors. A broad range of CD8(+) T-cell responses were observed and 6/7 donors had an immunodominant response against the relatively conserved internal nucleoprotein (NP). Dissecting the minimal epitope regions within the immunogenic NP led to the identification of six novel immunodominant epitopes, which include a 12-mer and an 8-mer peptides. The majority of immunodominant epitopes was clustered within the carboxyl terminal 2/3 of the NP protein and were highly conserved. We also subjected NP to three common computer algorithms for epitope prediction and found that most of the novel epitopes would not have been predicted. Our study emphasizes the importance of using a systematic approach to identify immunodominant CD8(+) T-cell responses and suggests that the epitope-rich regions within NP present a promising target for the T-cell-mediated multi-strain influenza vaccine.