gebhart/patrepeval huggingface dataset:
Efficient Decoding of the UAG Triplet as a Full-Fledged Sense Codon Enhances the Growth of a <i>prfA</i> -Deficient Strain of Escherichia coli (2012)

We previously reassigned the amber UAG stop triplet as a sense codon in Escherichia coli by expressing a UAG-decoding tRNA and knocking out the prfA gene, encoding release factor 1. UAG triplets were left at the ends of about 300 genes in the genome. In the present study, we showed that the detrimental effect of UAG reassignment could be alleviated by increasing the efficiency of UAG translation instead of reducing the number of UAGs in the genome. We isolated an amber suppressor tRNA(Gln) variant displaying enhanced suppression activity, and we introduced it into the prfA knockout strain, RFzero-q, in place of the original suppressor tRNA(Gln). The resulting strain, RFzero-q3, translated UAG to glutamine almost as efficiently as the glutamine codons, and it proliferated faster than the parent RFzero-q strain. We identified two major factors in this growth enhancement. First, the sucB gene, which is involved in energy regeneration and has two successive UAG triplets at the end, was expressed at a higher level in RFzero-q3 than RFzero-q. Second, the ribosome stalling that occurred at UAG in RFzero-q was resolved in RFzero-q3. The results revealed the importance of "backup" stop triplets, UAA or UGA downstream of UAG, to avoid the deleterious impact of UAG reassignment on the proteome.
Evaluation and management of benign esophageal strictures (2005)

Patients with progressive or solid food dysphagia should be evaluated for the presence of an esophageal stricture. Barium esophagram and endoscopy can define strictures as benign or malignant. The majority of benign strictures are acid-related. Benign strictures are best managed by esophageal dilation with acid-suppressing medications if a peptic stricture is suspected. If dysphagia recurs, repeat dilation should be performed. There are a variety of interventions for refractory strictures which include injection of intralesional corticosteroids, temporary placement of self-expanding plastic stents and surgery.
Quality Estimation: an experimental study using unsupervised similarity measures (2012)

We present the approach we took for our participation to the WMT12 Quality Estimation Shared Task: our main goal is to achieve reasonably good results without appeal to supervised learning. We have used various similarity measures and also an external resource (Google N-grams). Details of results clarify the interest of such an approach. 1
Detection for Conflicts of Dependencies in Advanced Transaction Models (2006)

Transactional dependencies play an important role in coordinating the execution of subtransactions in advanced transaction models, such as, nested transactions and workflow transactions. The correct execution of the advanced transactions depends on ensuring the satisfaction of all the dependencies, which are specified by the application developer. Incorrect specification of transaction dependencies might lead to information integrity problems and unavailability of resources. An example of incorrect specification of dependencies is the presence of conflicts - the satisfaction of constraints imposed by one dependency may violate the constraints imposed by another dependency. Algorithms that can analyze and detect dependency conflicts are necessary. Although a lot of research appears on advanced transactions, no previous work has been done on analysis of dependency conflicts. In this work, we analyze different kinds of dependency conflicts, propose algorithms to detect and remove the conflicts of dependencies in advanced transaction specifications. This will enable the application developer to get assurance about the correctness of the dependency specification and the correct behavior of the underlying advanced transaction model.
Systems metabolic engineering of <i>Escherichia coli</i> for <scp>L</scp> ‐threonine production (2007)

Amino-acid producers have traditionally been developed by repeated random mutagenesis owing to the difficulty in rationally engineering the complex and highly regulated metabolic network. Here, we report the development of the genetically defined L-threonine overproducing Escherichia coli strain by systems metabolic engineering. Feedback inhibitions of aspartokinase I and III (encoded by thrA and lysC, respectively) and transcriptional attenuation regulations (located in thrL) were removed. Pathways for Thr degradation were removed by deleting tdh and mutating ilvA. The metA and lysA genes were deleted to make more precursors available for Thr biosynthesis. Further target genes to be engineered were identified by transcriptome profiling combined with in silico flux response analysis, and their expression levels were manipulated accordingly. The final engineered E. coli strain was able to produce Thr with a high yield of 0.393 g per gram of glucose, and 82.4 g/l Thr by fed-batch culture. The systems metabolic engineering strategy reported here may be broadly employed for developing genetically defined organisms for the efficient production of various bioproducts.
Analysis of Thermodynamic Design Data for Cooling of Double -Effect Absorption System of Solar Energy using LiBr - water and Ethylene Glycol Mixture (2003)

For cooling of double effect absorption heat pump system of solar heating source, analysis of thermodynamic design data has been done to find the property of Libr-water + ethylene Glycol mixture for working fluid by computer simulation. Derived thermodynamic design data, enthalpy based coefficient of performance and flow ratio for possible combinations of operating temperature for water - LiBr and Ethylene Glycol mixture ( : CHO ratio 10:1 by mole) by computer simulation are done. The obtained results, COP and mass flow ratio of the water - lithium bromide - ethylene glycol system, are compared with data for the water-Libr pair solution.
A randomized controlled clinical trial of topical photodynamic therapy with methyl aminolaevulinate in the treatment of actinic keratoses in transplant recipients (2004)

Photodynamic therapy using methyl aminolaevulinate is a safe and effective treatment for actinic keratoses in transplant recipients. It may also reduce the risk of transformation of actinic keratoses to invasive, potentially fatal, squamous cell carcinoma.
Decision-feedback equalization for CDMA downlink (2003)

A well-known receiver strategy for a linearly modulated signal transmitted over a frequency-selective channel is channel equalization. Recently it was proposed to employ a minimum mean-squared error (MMSE) channel equalizer for the downlink of CDMA. In this paper, we introduce a new receiver concept using MMSE channel equalization as a first stage and MMSE decision-feedback equalization (DFE) utilizing soft feedback from the decoding unit as a second stage. Both schemes are compared for the downlink of CDMA. It turns out, that after channel decoding we gain about 1 dB compared to conventional MMSE channel equalization.
The major subunit of <i>Escherichia coli</i> type 1 fimbriae is not required for D‐mannose‐specific adhesion (1990)

Type 1 fimbriae are surface organelles on Escherichia coli, which mediate specific binding to D-mannose-containing structures. These fimbriae are heteropolymers composed of a major building element, the FimA protein, and small amounts of the FimF, FimG and FimH proteins. The FimH protein is uniquely responsible for the D-mannose receptor binding. In this work data are presented which indicate that the major subunit of type 1 fimbriae is dispensable for D-mannose-specific binding. A recombinant strain was studied which harboured an insertional deletion in the fimA gene, and was thereby unable to produce type 1 fimbriae; however, it was still able to express a D-mannose-binding phenotype. However, the deletion resulted in a 25-fold reduction of the adhesive potential, as measured by binding to D-mannose-coated Sepharose beads. Serological and specific receptor binding evidence is presented that suggests that the FimH adhesion is capable of being exposed on the bacterial surface without being an integral part of the fimbriae.
FACILE SYNTHESIS OF ARYL CYANIDES FROM IODIDES CATALYZED BY PALLADIUM TRIPHENYLPHOSPHINE COMPLEX (1975)

Abstract Cyanogenation of iodobenzene with potassium cyanide has been found to proceed smoothly in tetrahydrofuran in the presence of a catalytic amount of tetrakis(triphenylphosphine)palladium(O). The reaction involves an intermediate, iodo(phenyl)bis(triphenylphosphine)palladium(II), which acts as a retracing species in the catalytic reaction path.
Pyroelectric infrared sensor using PZT thin plate on diaphragm as sensitive elements (1996)

Abstract To improve performance characteristics of a pyro‐electric infrared sensor, especially voltage responsivity ( R v ), noise equivalent power (NEP), and response speed, it is necessary to reduce the heat capacity of an infrared sensing element which is made of Pb(Zr, Ti)O 3 (PZT) ceramics. A new design for a sensor whose sensing element is made of a thin bulk PZT ceramic plate mounted on a diaphragm fabricated by the Si micromachining method has been proposed and its prototypes have been tested. The prototype sensor has a PZT ceramic plate which is about 10‐μm thick and has a sensing area of 1 × 2 mm 2 . The new sensor has an R v value of 36.3 to 37.9 mV/μW which is about five times higher than a pyroelectric sensor with a 100‐μm thick PZT bulk ceramic plate. The amount of sensor noise was expected to be reduced by half. However, the amount of sensor noise increased by a factor of two. Because of the increase in the sensor noise, the values of NEP were 1.8 to 3.3 × 10 −2 μW, which is a factor of two to three smaller than the NEP value of the bulk sensor. Furthermore, the rise time decreased to 31 to 35 ms, which is 10 to 20 percent shorter than that of the bulk sensor. Thus, the reduction of sensor noise will be an important challenge for the future.
The Effects of Differentiated Instruction and Enrichment Pedagogy on Reading Achievement in Five Elementary Schools (2010)

This experimental study examined the effect of a differentiated, enriched reading program on students’ oral reading fluency and comprehension using the schoolwide enrichment model–reading (SEM-R). Treatment and control conditions were randomly assigned to 63 teachers and 1,192 second through fifth grade students across five elementary schools. Using multilevel modeling, significant differences favoring the SEM-R were found in reading fluency in two schools (Cohen’s d effect sizes of .33 and .10) and in reading comprehension in the high-poverty urban school (Cohen’s d = .27), with no achievement differences in the remaining schools. These results demonstrate that an enrichment reading approach, with differentiated instruction and less whole group instruction, was as effective as or more effective than a traditional whole group basal approach.
DNA‐based monitoring of total bacterial community structure in environmental samples (1995)

Determining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between micro-organisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA-binding dye bisbenzimidazole which imposes G+C-dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G+C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.
In-vitro activity of voriconazole (UK-109,496), LY303366 and other antifungal agents against oral Candida spp. isolates from HIV-infected patients (1999)

In this report we compare the activity of two new antifungal agents, voriconazole (UK-109,496) and LY303366 with the activities of other antifungals including fluconazole, itraconazole, 5-fluorocytosine (5FC) and amphotericin B against 219 oral Candida spp. isolates from HIV-infected patients. We used the broth microdilution method following the guidelines of the NCCLS. The in-vitro activity of voriconazole (UK-109,496) (MIC(90) 0.12 mg/L) and LY303366 (CMI(90) 0.25 mg/L) against clinical isolates of Candida spp. was excellent and comparable with that of amphotericin B (MIC(90) 0.5 mg/L), and better than those of fluconazole (MIC(90) > or = 64 mg/L), itraconazole (MIC(90) 4 mg/L) and 5FC (MIC(90) 1 mg/L).
Disruption of the transcription factor recombination signal‐binding protein‐Jκ (RBP‐J) leads to veno‐occlusive disease and interfered liver regeneration in mice† (2008)

Notch/RBP-J signaling may play dual roles in LSECs: in resting liver it represses proliferation, and in regenerating liver it supports proliferation and functional differentiation.
Towards improving the drought tolerance of rice in China (2006)

Drought tolerance (DT) is a very complex trait. For the purpose of developing DT rice cultivars, a research programme was initiated in 1997 in China, consisting of four coherent parts: the development of a DT field screen facility and evaluation standard; the collection, evaluation and enhancement of DT rice resources; DT gene/quantitative trait locus (QTL) discovery; and DT rice breeding. More than 2000 rice accessions, mostly from China, were collected and evaluated in a new DT screening facility with a powerful water management system. Eighty-six entries were selected to serve as a core DT collection. A set of 187 recombinant inbred lines was developed for the genetic mapping of DT and high yield-related QTL under drought conditions. Several DT rice cultivars adapted to southern and central China were released. DT rice CMS lines were developed and distributed to most parts of China to encourage the development of DT or water-saving hybrid rice.
Dextran-conjugated anti-Ig antibodies as a model for T cell-independent type 2 antigen-mediated stimulation of Ig secretion in vitro. I. Lymphokine dependence (1991)

We have previously demonstrated that dextran-conjugated anti-IgD antibodies (anti-delta-dex) stimulate high levels of B cell proliferation at concentrations that are 1000-fold lower than that required by unconjugated anti-Ig. We now show that anti-delta-dex may provide a suitable model to study Ig secretion stimulated by soluble T cell-independent type 2 Ag exemplified by TNP-Ficoll. Thus, both TNP-Ficoll and anti-delta-dex stimulate low to undetectable levels of Ig secretion when cultured with resting B cells. Addition of IL-5 or IL-2 stimulated enhanced anti-TNP responses in the presence of TNP-Ficoll, or induced polyclonal Ig secretion in the presence of anti-delta-dex. Both TNP-Ficoll and anti-delta-dex conjugates stimulated Ig production by Percoll-separated low density (partially activated) B cells in the absence of added lymphokines. These findings point to the similarities in the activation requirements of TNP-Ficoll and anti-delta-dex and suggest that dextran-anti-Ig conjugates, which can induce B cell activation irrespective of Ag specificity, may provide a useful model for studying various parameters that characterize the responses to soluble TI type 2 Ag.
An introduction to aqueous electrolyte solutions (2007)

Preliminary Chapter Guidance to Students. Chapter 1: Concepts and Ideas: Setting the Stage. Chapter 2: The Concept of Chemical Equilibrium: An Introduction. Chapter 3: Acids and Bases: A First Approach. Chapter 4: Equilibrium Calculations for Acids and Bases. Chapter 5: Equilibrium Calculations for Salts and Buffers. Chapter 6: Neutralisation and pH curves. Chapter 7: Ion Pairing, Complex Formation and Solubilities. Chapter 8: Practical Applications of Thermodynamics for Electrolyte Solutions. Chapter 9: Electrochemical Cells and EMFs. Chapter 10: Concepts and Theory of Non-ideality. Chapter 11: Conductance: The Ideal Case. Chapter 12 Conductance: The Non-ideal Case for Symmetrical Electrolytes. Chapter: 13 Solvation.
Methods for determining proximity to voltage collapse (1991)

Theoretical results have shown that PQ controllability is sufficient to insure that every known test for prevention of voltage collapse is satisfied. This result unifies the theoretical basis for voltage collapse, since these tests were developed based on radically different power system models, tested very different matrices and conditions, and were based on different theoretical approaches. This theoretical foundation is used to develop methods of determining the proximity to voltage collapse. An algorithm for computing voltage control areas, which are groups of interconnected buses, is developed. It is shown that proper system and operation planning must be undertaken in each voltage control area if voltage collapse is to be prevented. A measure of the proximity to voltage collapse is shown to be the reactive reserves in a voltage control area boundary.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Model demonstrates functional purpose of the nasal cycle (2015)

It is quantitatively demonstrated in this work how the nasal cycle enables the upper airway to accommodate the contrasting roles of air conditioning and the removal of entrapped contaminants through fluctuation in airflow partitioning between each airway.
Biological activity of a growth hormone-releasing factor secreted by a human tumor (1983)

A substance released by a pancreatic islet cell tumor induced signs and symptoms of acromegaly in a young woman. The culture medium in which the tumor was placed after resection was added to rat anterior pituitary cells and incubated in vitro. Both newly synthesized and total rat growth hormone (GH) release as well as cellular cyclic AMP accumulation were stimulated in a dose-dependent manner by the tumor medium. Coincubation with somatostatin blocked these effects. The increase of cyclic AMP preceded the enhanced GH release, indicating that cyclic AMP may be a second messenger for the tumor factor(s). Neither prolactin nor luteinizing hormone secretion was affected by the tumor medium. When measured by a perfused cell column apparatus, there was a rapid and dramatic release of GH by the dispersed rat pituitary cells during a 2.5-, 10-, and 40-min pulse of tumor medium; both the onset and termination of the GH response reached maximal or control values, respectively, within 5 min. Pretreatment of the tumor medium with pepsin markedly attenuated the tumor medium activity, indicating the peptide nature of the factor(s). Finally, ultrastructural analysis indicated that the somatotrophs were degranulated by the tumor medium, whereas there was no similar effect apparent on the mammotrophs. Whether this tumor polypeptide is identical to native hypothalamic GH-releasing hormone remains to be proved.
Fetal Cardiac Doppler Signal Processing Techniques: Challenges and Future Research Directions (2017)

The fetal Doppler Ultrasound (DUS) is commonly used for monitoring fetal heart rate and can also be used for identifying the event timings of fetal cardiac valve motions. In early-stage fetuses, the detected Doppler signal suffers from noise and signal loss due to the fetal movements and changing fetal location during the measurement procedure. The fetal cardiac intervals, which can be estimated by measuring the fetal cardiac event timings, are the most important markers of fetal development and well-being. To advance DUS-based fetal monitoring methods, several powerful and well-advanced signal processing and machine learning methods have recently been developed. This review provides an overview of the existing techniques used in fetal cardiac activity monitoring and a comprehensive survey on fetal cardiac Doppler signal processing frameworks. The review is structured with a focus on their shortcomings and advantages, which helps in understanding fetal Doppler cardiogram signal processing methods and the related Doppler signal analysis procedures by providing valuable clinical information. Finally, a set of recommendations are suggested for future research directions and the use of fetal cardiac Doppler signal analysis, processing, and modeling to address the underlying challenges.
DETERMINATION OF SUGARS IN AQUEOUS MIXTURES USING MID-INFRARED SPECTROSCOPY (2000)

The combination of mid-infrared (MIR) spectroscopy and multivariate statistics for determination of glucose,fructose, and sucrose in aqueous mixtures was investigated. Spectra of different samples were recorded in the MIR rangebetween 400 and 4000 nm. Aqueous mixtures of 10, 20, and 40% total sugars with different combinations of glucose,fructose and sucrose were used for calibration and validation studies. Spectral wavenumber region from 700 to1530 cm 1 was selected for Principal Component Regression (PCR) and Partial Least Square regression (PLS) to developcalibration models for sugar content determination (%, w/v) in liquid foods. Results from the PLS-1 (first derivative)models were slightly better than those obtained with other used calibration models. Merging of the 10, 20, and 40%calibration data into single calibration set enabled the prediction (average standard error of calibration, SEC = 0.34) ofindividual sugars in the entire range accurately. The squared correlation (R 2 ) values for the calibrated models forglucose, fructose and sucrose were 0.997, 0.998, and 0.997, respectively, between the predicted values and actual values.The calibrations were successfully applied to predict sugar contents in complex mixtures and commercial beverages.Results indicated that fourier transform infrared (FTIR) spectroscopy can be used for rapid detection of sugars incomplex mixtures.
Growth of <i>Helicobacter pylori</i> in Medium Supplemented with Cyanobacterial Extract (2003)

Solid and liquid media supplemented only with a cyanobacterial extract (CE) and free of fetal calf serum (FCS), blood, and its derivatives support the growth of Helicobacter pylori. A total of 11 strains of H. pylori isolated from gastric biopsy samples were successfully subcultured in Mueller-Hinton agar supplemented with 0.4% CE. When this medium was used for primary isolation of H. pylori, a low isolation rate (30%) was observed because of the abundant growth of contaminants. The growth kinetics of eight isolates and H. pylori reference strain NCTC 11638 in Mueller-Hinton broth (MHB) supplemented with 0.7% CE were estimated by use of growth parameters, and the results were compared with those obtained with MHB-5% FCS. For four strains the cellular concentrations obtained with CE were statistically higher (P < 0.05) than those obtained with FCS, and in some cases these values were similar to the highest values reported in the literature. Depending on the strain, the specific growth rates obtained with CE were similar to or increased compared with those obtained with FCS. The replacement of FCS by CE in H. pylori cultures would facilitate the retrieval of cultures with high cellular densities as a source of cellular and extracellular proteins free of serum. Also, CE has advantages over conventional supplements, such as easier conservation and compliance with the pressing tendency at present to avoid the use of products derived from animals.