gebhart/patrepeval huggingface dataset:
Editing modifies the GABAA receptor subunit  3 (2007)

Adenosine to inosine (A-to-I) pre-mRNA editing by the ADAR enzyme family has the potential to increase the variety of the proteome. This editing by adenosine deamination is essential in mammals for a functional brain. To detect novel substrates for A-to-I editing we have used an experimental method to find selectively edited sites and combined it with bioinformatic techniques that find stem-loop structures suitable for editing. We present here the first verified editing candidate detected by this screening procedure. We show that Gabra-3, which codes for the alpha3 subunit of the GABA(A) receptor, is a substrate for editing by both ADAR1 and ADAR2. Editing of the Gabra-3 mRNA recodes an isoleucine to a methionine. The extent of editing is low at birth but increases with age, reaching close to 100% in the adult brain. We therefore propose that editing of the Gabra-3 mRNA is important for normal brain development.
An Attitude Compensation Technique for a MEMS Motion Sensor Based Digital Writing Instrument (2006)

A MAG-muIMU which is based on MEMS gyroscopes, accelerometers, and magnetometers is developed for real-time estimation of human hand motions. Appropriate filtering, transformation and sensor fusion techniques are combined in the ubiquitous digital writing instrument to record handwriting on any surface. In this paper, we discuss the design of an extended Kalman filter based on MAG-muIMU (micro inertial measurement unit with magnetometers) for real-time attitude tracking. The filter utilizes the gyroscope propagation for transient updates and correction by reference field sensors, such as gravity sensors, magnetometers or star trackers. A process model is derived to separate sensor bias and to minimize wideband noise. The attitude calculation is based on quaternion which, when compared to Euler angles, has no singularity problem. Testing with synthetic data and actual sensor data proved the filter will converge and accurately track the attitude of a rigid body. Our goal is to implement this algorithm for motion recognition of a 3D ubiquitous digital pen.
Reduction of Microbial Counts at a Commercial Beef Koshering Facility (1999)

ABSTRACT Effectiveness of a water soaking, salting, and water rinsing (koshering) process in reducing microbial counts was examined. Beef briskets (30) were sampled at four stages in the plant, viz. prewashing, postwashing, after 24 h chilling, and after koshering. Quantitative aerobic plate, coliforms, and Escherichia colicounts, and qualitative analysis for Salmonella were determined. PROC MIXED and GLM procedures were applied to determine statistical differences among least square means (LSM) at p.0.05. Microbial counts did not always decrease from prewashing to postwashing, after 24 h chilling, or after koshering but koshering reduced APC, coliforms, and E. coli from initial counts. Salmonella were also reduced.
Boundary-Layer Transition Experiments on Pre-Ablated Graphite Nosetips in a Hyperballistics Range (1977)

Abstract : An experimental program was conducted to test the validity of extrapolating the PANT (Passive Nosetip Technology) boundary-layer transition correlation, based on wind-tunnel/calorimeter-model results, to actual nosetip materials exposed to actual reentry environments. Pre-ablated ATJ-S graphite nosetips were flown on specific ballistics range trajectories through both air and nitrogen (with and without ablation). Surface temperature contours were measured via electrooptical pyrometry, from which transition zone presence and location were inferred. Significant discrepancies were noted between predicted and experimentally observed transition zone behavior, as influenced by Reynolds number and wall-temperature effects. A question was raised concerning characterization of a surface microroughness distribution, for transition purpose, by its median value. In addition, significant surface roughness effects on laminar-flow heat-transfer rates were noted.
Abstract P103: Impairment of Lower Extremity Physical Performance in Non-Dialysis CKD. (2012)

Background: Kidney dysfunction leads to the retention of metabolic waste products which may subsequently impair muscle function and physical performance. Methods: We prospectively measured physical performance in 183 stroke-free older adults with stage 3-4 CKD to determine the pattern of functional impairment and the relationship of performance with severity of CKD. Functional tests included the short physical performance battery (SPPB), 4 meter walk (gait speed), 6 minute walk distance (6MWD), timed get up and go test (TGUAG), grip strength, and peak expiratory flow. Physical performance in the CKD cohort was compared to normative data obtained from 78 non-CKD controls for the TGUAG and to expected performance from published normative data for other performance measures. Among CKD subjects, associations of performance with eGFR and proteinuria were estimated using linear regression adjusting for age, sex, race, height, and weight. Results: Mean eGFR was 34.8 ±12.5 mL/min/1.73m 2 , mean BMI 30.6 ±6 kg/m 2 , and median proteinuria 240 mg/g. Mean age was 66 ±7.7years, 91% were male, 33% African American, and 40% diabetic. CKD patients had significantly worse performance compared to predicted values on the TGUAG test (36 ±41% slower), gait speed (-31.7 ±15%), 6MWD (-31 ±15%), and peak expiratory flow (-25 ±34%). Among CKD subjects, lower eGFR and greater proteinuria were associated with worse performance on the 6MWD ( Table ). In contrast, no significant associations were observed between eGFR or proteinuria with performance on the other physical performance tests. Renal Function Measure 6 Meter Walk Distance (meters) Units β * (95%CI) P value GFR MDRD (mL/min/1.73m 2) 10mL/min/1.73m 2 decrement −11.0 (-23.0, 1.1) 0.07 45-59 Ref 30-44 −7.0 (-38, 24) .044 <30 −35 (-68, -1.3) Proteinuria (mg/g Cr) 1 ln-increment −11.0 (-21.1, -0.9) 0.033 0-299 Ref ≥300 −25.8 (-53, 1.38) 0.063 * Adjusted for age, sex, race, height, and weight Conclusions: Older adults with CKD exhibit markedly reduced physical performance, especially for tests of lower extremity function. Lower renal function and greater proteinuria are associated with worse performance on the 6-minute walk test, a measure of submaximal gait.
Universal DNA tag systems (2000)

Custom-designed DNA arrays offer the possibility of simultaneously monitoring thousands of hybridization reactions These arrays show great potential for many medical and scientific applications such as polymorphism analysis and genotyping. Relatively high costs are associated with the need to specifically design and synthesize problem specific arrays. Recently, an alternative approach was suggested that utilizes fixed, universal arrays. This approach presents an interesting design problem—the arrays should contain as many probes as possible, while minimizing experimental errors caused by cross-hybridization. We use a simple thermodynamic model to cast this design problem in a formal mathematical framework. Employing new combinatorial ideas, we derive an efficient construction for the design problem, and prove that our construction is near-optimal.
Preparation of 1-acyloxyethyl esters of 7-(2-(2-aminothiazol-4-yl)acetamido)-3-(((1-(2-dimethylaminoethyl)-1H-tetrazol-5-yl)thio)methyl)ceph-3-em-4-carboxylic acid (cefotiam) and their oral absorption in mice. (1986)

In a separate study on the orally active acyloxymethyl esters (1) of 7-[2-(2-aminothiazol-4-yl)acetamido]-3-[[[1-(2-dimethylaminoethyl) - 1H-tetrazol-5-yl]thio]methyl]ceph-3-em-4-carboxylic acid (cefotiam, CTM), we have shown, by quantitative structure-oral bioavailability (BA) relation analysis, that the R2 group in the acyl group R2CO must have both an adequate lipophilicity (Hansch's lipophilic parameter, pi) and steric hindrance (Taft's Es value). However, to satisfy these requirements, a complex alkyl group R2 must be employed, the ester of which is difficult to synthesize and has unique metabolic fate. In this study, we selected and prepared the 1-acyloxyethyl esters (2) of CTM instead of 1 to avoid R2 groups that are too complicated. We found that the esters (2) gave improved oral BAs over 1: the 1-(3-methyl-valeryloxy)ethyl ester (2h) showed the highest peak plasma CTM level (Cmax) comparable to that obtained after subcutaneous injection of CTM. The 1-(cyclohexylacetoxy)ethyl ester (2t), the 1-(2-ethylbutyryloxy)ethyl ester (2j), and 2h showed BAs near 100%. For these esters (2), good correlations were also observed among the pi, the Es values of R2, and the log Cmax and log BA in the analysis of the quantitative structure-oral bioavailability relation: an ester having an alkyl group as R2 with a pi value of 3.07 or 3.08 and a Es value of -1.04 or -1.29 gave the highest Cmax or BA, respectively. As expected, the optimal pi values are almost the same as those obtained with 1 but the optimal Es values are larger (Es = -2.07). Thus, it has been confirmed by preparing 1-acyloxyethyl esters (2) of CTM that the oral bioavailability of CTM can further be improved without preparing acyloxymethyl esters (1) with a complicated acyl group.
Ocular Angiogenesis: Vascular Endothelial Growth Factor and Other Factors (2015)

Systematic study of the mechanisms underlying pathological ocular neovascularization has yielded a wealth of knowledge about pro- and anti-angiogenic factors that modulate diseases such as neovascular age-related macular degeneration. The evidence implicating vascular endothelial growth factor (VEGF) in particular has led to the development of a number of approved anti-VEGF therapies. Additional proangiogenic targets that have emerged as potential mediators of ocular neovascularization include hypoxia-inducible factor-1, angiopoietin-2, platelet-derived growth factor-B and components of the alternative complement pathway. As for VEGF, knowledge of these factors has led to a product pipeline of many more novel agents that are in various stages of clinical development in the setting of ocular neovascularization. These agents are represented by a range of drug classes and, in addition to novel small- and large-molecule VEGF inhibitors, include gene therapies, small interfering RNA agents and tyrosine kinase inhibitors. In addition, combination therapy is beginning to emerge as a strategy to improve the efficacy of individual therapies. Thus, a variety of agents, whether administered alone or as adjunctive therapy with agents targeting VEGF, offer the promise of expanding the range of treatments for ocular neovascular diseases.
Study of Dominant Performance Characteristics in Robot Transmissions (1993)

Six different transmission types suitable for robotic manipulators were compared in an experimental and theoretical study. Single-degree-of-freedom mechanisms based on the different transmissions were evaluated in terms of force control performance, achievable bandwidth, and stability properties in hard contact tasks. Transmission types considered were (1) cable reducer, (2) harmonic drive, (3) cycloidal disk reducer, (4) cycloidal cam reducer, (5) ball reducer, and (6) planetary/cycloidal gear head. Open loop torque following error, attenuation and phase lag, and closed loop bandwidth and stability margin were found to be severely dominated by levels of inertia, stiffness distribution and variability, stiction, coulomb and viscous friction, and ripple torque. These aspects were quantified and shown to vary widely among all transmissions tested. The degree of nonlinearity inherent in each transmission affected its open and closed loop behavior directly, and limited the effectiveness of controller compensation schemes. Simple transmission models based on carefully measured transmission characteristics are shown to predict stability margins and achievable force-control bandwidths in hard contact to within a 5 to 15 percent error margin.
Microbial Dark Matter Phase II: Stepping deeper into unknown territory (2014)

Currently available microbial genomes are of limited phylogenetic breadth due to ourhistorical inability to cultivate most microorganisms in the laboratory. The firstphase of the Microbial Dark Matter project used single-cell genomics to sequence 201single cells from uncultivated lineages, and was able to resolve new superphyla andreveal novel metabolic features in bacteria and archaea. However, many fundamentalquestions about the evolution and function of microbes remain unanswered, and manycandidate phyla remain uncharacterized. Phase II of the Microbial Dark Matter projectwill target candidate phyla with no sequenced representatives at a variety of new sites usinga combination of single-cell sequencing and shotgun metagenomics approaches.
Pulsed‐Potential Oxidation of Methanol: II . Graphite‐Supported Platinum Electrode With and Without Tin Surface Modification (1992)

Pulsed‐potential control is examined as an alternative to steady‐state (dc) operation as a means of increasing the oxidation rate of methanol on a graphite‐supported Pt electrode, with and without surface modification by Sn. The potential was pulsed from a low polarization (of duration ), at which methanol oxidation and poison formation occur, to a high polarization (of duration ), at which the poison is oxidatively removed; the effects of varying , , and were studied. The electrodes were prepared by ion‐exchange of onto an electro‐oxidized graphite followed sequentially by air activation and electrochemical reduction. The surface area was measured during extensive pulse‐ and triangle‐waveform polarization and decreased but remained stable at 70% of the initial value. From SEM photographs, platinum redistribution into the porous graphite and particle agglomeration were found. The time‐averaged methanol current density using the pulsed‐control strategy was significantly higher in comparison to dc control. The current density without Sn modification at (vs. RHE) increased one order‐of‐magnitude above the dc value of 0.1 mA/cm2, with current density based upon the measured Pt area; at , a four orders‐of‐magnitude increase was found above the dc value of 0.1 μA/cm2. The methanol oxidation current at 0.6 and 0.4 V using the optimum concentration of was only 10–50% higher than that obtained without it under the same pulsed control. X‐ray photoelectron spectroscopy (XPS) was used to characterize the effect of pulsed‐potential control on the oxidation states of the platinum. The pulsed electrolysis enhanced the chemical interaction between the platinum crystallites and the graphite substrate and increased the platinum oxide coverage.
Effects of Intraabdominanlly Insufflated Carbon Dioxide and Elevated Intraabdominal Pressure on Splanchnic Circulation  (1998)

In contrast to air insufflation, intraabdominal insufflation of CO2 resulted in a moderate splanchnic hyperemia at an intraabdominal pressure < or = 12 mmHg. At higher intraabdominal pressure values, pressure-induced changes became more important than the type of gas used.
Development of advanced NO{sub x} control concepts for coal-fired utility boilers. Quarterly technical progress report No. 1, September 26--December 31, 1990 (1991)

Hybrid technologies for reduction of NO{sub x} emissions from coal fired utility boilers may offer greater levels of NO{sub x} control than the sum of the individual technologies, leading to more cost effective emissions control strategies. Energy and Environmental Research Corporation had developed a hybrid NO{sub x} control strategy involving two proprietary concepts which has the potential to meet the US Department of Energy`s goal at a significant reduction in cost compared to existing technology. The process has been named CombiNO{sub x}. CombiNO{sub x} is the integration of three separate NO control technologies: (1) Gas Reburning, (2) CO-Promoted Selective Non-Catalytic Reduction, and (3) Methanol Injection/NO{sub 2} Scrubbing.
Wide-band lumped circuit model of the terminal and internal electromagnetic response of a coil with a coaxial insulation system (2002)

A wide-band lumped circuit model of a coil with a coaxial insulation system is presented, which can be used to simulate the terminal and internal electromagnetic response. The frequency response of the lumped circuit is experimentally verified up to a few MHz. The circuit parameters are based on data concerning the geometry and materials. The capacitive and resistive response of the insulation system is considered thoroughly, as it is very different from a conventional winding. The model is of special interest for electromagnetic power devices with a coaxial insulation system, e.g. PowerformerTM and DryformerTM.
Adrenomedullin Increases Inducible Nitric Oxide Synthase in Rat Vascular Smooth Muscle Cells Stimulated With Interleukin-1 (1996)

We investigated the effects of adrenomedullin on nitric oxide synthesis by measuring the production of nitrite, a stable metabolite of nitric oxide, in cultured rat vascular smooth muscle cells. Incubation of cultures with interleukin-1beta (10 ng/mL) for 24 hours caused a significant increase in nitrite generation. The interleukin-1beta-induced nitrite production by vascular smooth muscle cells was significantly increased by adrenomedullin in a dose-dependent manner (10(-10) to 10(-6) mol/L). This effect of adrenomedullin was significantly inhibited in the presence of Ng-monomethyl-L-arginine. The adrenomedullin-induced nitrite production by interleukin-1beta-stimulated cells was accompanied by increased inducible nitric oxide synthase mRNA accumulation. In the presence of the phosphodiesterase inhibitor isobutylmethylxanthine, interleukin-1beta-induced nitrite accumulation was further increased, but the effect of adrenomedullin was not additive or synergistic. Adrenomedullin dose dependently increased intracellular cAMP levels of vascular smooth muscle cells. These results indicate that adrenomedullin augments nitric oxide synthesis in interleukin-1beta-stimulated vascular smooth muscle cells, at least partially through a cAMP-dependent pathway.
Reduced temperature sensitivity of lasing wavelength in near-1.3 µm InAs/GaAs quantum-dot laser with stepped composition strain-reducing layer (2007)

An InGaAs strain-reducing capping layer with a stepped composition is shown to significantly reduce the temperature sensitivity of the lasing wavelength in a 1.3 µm InAs/GaAs quantum-dot laser. With this technique, the sensitivity is reduced from 0.48 nm/K for a laser with standard capping layer to 0.11 nm/K for the new design over the temperature range 20–130°C.
Screening of a Small Set of Random Peptides: A New Strategy to Identify Synthetic Peptides that Mimic Epitopes (1997)

Small diversity libraries, composed of 4550 synthetic dodecapeptides and 8000 synthetic tripeptides, have been used to identify sequences homologous to small linear and non-linear parts of epitopes. Here we report that synthetic peptides identified through alignment of dodecapeptides and tripeptides derived from these small libraries have, in direct ELISA and/or competitive ELISA, activities similar to that of peptides covering the native epitope and similar to that of peptides derived from large expression libraries composed of 106–107 random peptides. This result was obtained with the monoclonal antibodies 6A.A6 and M2. Mab 6A.A6 binds the transmissible gastroenteritis virus (TGEV) and mAb M2 binds the FLAG®-peptide, an affinity tag. It was also found that the antibody binding activity of peptides, derived from small or large libraries, can strongly depend on the way in which the peptide is presented to the antibody, i.e. high antibody titers were obtained when these peptides were synthesized on pins or coated onto microtiter plates, whereas low IC50s were obtained with these peptides in solution. We postulate that small peptide libraries may be a powerful tool to quickly identify new peptides that can be used as sensitive markers for mAbs of interest. © 1997 John Wiley & Sons, Ltd.
Metabolism of .GAMMA.-linolenic acid in primary cultures of rat hepatocytes and in Hep G2 cells. (1989)

Incorporation and metabolism of gamma-linolenic acid (GLA) in both rat hepatocytes and Hep G2 cells were compared to those of oleic (OA), linoleic (LA), alpha-linolenic (LLA), and dihomo-gamma-linolenic (DGLA) acids. The incorporation of GLA into both types of cells was higher than LLA and DGLA, but lower than OA and LA. It was efficiently converted into DGLA in both types of cells and increased the concentration of DGLA. LLA was converted to a small amount of C20:4 (n-3) only in Hep G2 cells. Incubation with LA, GLA, LLA, and DGLA did not increase the concentration of arachidonic acid (AA) in both types of cells. LA. GLA, LLA, and their metabolites were incorporated into phosphatidylcholine, but only GLA and its metabolite, DGLA, were also incorporated into phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol. The coexistence of GLA and LLA during their catabolism diminished the amounts of respective metabolite in Hep G2 cells. The presence of GLA inhibited completely the formation of C20:4(n-3) from LLA. The results indicate that GLA is more effective in raising the ratio of DGLA/AA. Also, polyunsaturated fatty acids of n-3 and n-6 series have competitively catabolized in both types of hepatocytes.
DERIVATE DES PHOSPHORSÄURE-o-PHENYLENESTERS. 20. (1982)

Abstract The halogenation of phenyl-and o-methoxyphenyl-o-phenylene phosphites (1b, 1c) gives at low temperature pentacoordinated dihalogenophosphoranes 4a, 4b, 5a, 5b. They are stable at room temperature with the exception of 5b. Even at-100°C 5b slowly gives a bromospirophosphorane 3b by breaking the ether linkage. The primary formed phosphorane is in an equilibrium with the phosphoniumsalt; both phosphorus compounds are proved with 31P n.m.r. spectroscopy. Die Halogenierung von Phenyl-und o-Methoxyphenyl-o-phenylenphosphit (1b, 1c) führt bei tiefen Temperaturen zu pentakoordinierten Dihalogenophosphoranen 4a, 4b, 5a, 5b, die beim Erwärmen auf Raumtemperatur mit Ausnahme von 5b stabil sind. Aus 5b entsteht bereits bei-100°C langsam unter Etherspaltung ein Spirophosphoran 3b. Das primär gebildete Phosphoran liegt mit dem Phosphoniumsalz im Gleichgewicht vor; beide Phosphorverbindungen sind NMR-spektroskopisch nachweisbar.
<i>dr</i> and <i>spr/sr</i> mutations of <i>Chlamydomonas reinhardtii</i> affecting D1 protein function and synthesis define two independent steps leading to chronic photoinhibition and confer differential fitness (1997)

ABSTRACT The effects of introduced chloroplast gene mutations affecting D1 synthesis, turnover and function on photosynthesis, growth and competitive ability were examined in autotrophic cultures of Chlamydomonas reinhardtii (Chlorophyta) adapted to low or high irradiance. Few discernible effects were evident when the mutants were grown in low light (LL, 70 μmol m −2 s −1 ). The herbicide‐resistant psbA mutation Ser 264 → Ala ( dr ) slowed electron transfer and accelerated D1 degradation in cells grown under high light (HL, 600 μmol m −2 s −1 ). The maximum rate of light‐and CO 2 ‐saturated photosynthesis, cell growth rate and competitive ability in the dr mutant were reduced compared to wild type under HL. However, the wild‐type rate of D1 synthesis in dr was adequate to compensate for accelerated D1 degradation. 16S rRNA mutations conferring resistance to streptomycin and spectinomycin ( spr/sr ) that altered chloroplast ribosome structure and assembly were used to inhibit chloroplast protein synthesis. In spr/sr cells grown under HL, D1 synthesis was reduced by 40–60% compared to wild type and D1 degradation was accelerated, leading to a 4‐fold reduction in D1 pool size. The reduced D1 levels were accompanied by an elevation of F o and a decline in F v / F m , quantum yield and maximum rate of CO 2 ‐saturated photosynthesis. Chemostat experiments showed that the growth rate and competitive ability of spr/sr were reduced against both wild type and dr.