gebhart/patrepeval huggingface dataset:
Overexpression, Purification, and Analysis of Complementation Behavior of <i>E. coli</i> SuhB Protein:  Comparison with Bacterial and Archaeal Inositol Monophosphatases (2000)

The E. coli suhB gene product, which has been suggested to participate in posttranscriptional control of gene expression, also possesses inositol-1-phosphatase (I-1-Pase) activity. To test if SuhB I-1-Pase activity is sufficient for its function in cells, we have cloned the genes for three other I-1-Pases (from the archaea Methanococcus jannaschii and Archaeoglobus fulgidus, and from the bacterium Thermotoga maritima) into the E. coli expression vector pET23a(+) and examined if these extragenic I-1-Pases could complement the suhB mutation in E. coli strain CG1307 (which also has a mutation in dnaB and a cold-sensitive phenotype). None of these I-1-Pase genes restored growth at 30 degrees C although they generated active I-1-Pase enzymes (as measured by I-1-Pase specific activities of crude protein extracts from the transformed CG1307 cells). In contrast, the pET23a(+) recombinant plasmid with the wild-type E. coli suhB gene complemented the cold sensitivity of the chromosomal mutant suhB and restored the temperature-sensitive growth of the dnaB mutation in the double mutant strain CG1307. Further evidence that this relief of the suppressor behavior of the suhB mutation is not related to the I-1-Pase activity of the SuhB protein was provided by construction of the E. coli SuhB mutant D87N. This mutant protein is inactive as an I-1-Pase but fully functional in changing the temperature sensitivity of the E. coli double mutant strain. Therefore, I-1-P phosphatase activity is neither sufficient nor required for complementation of suhB mutant suppressor effects. The wild-type E. coli SuhB protein was also overexpressed to very high levels and purified to homogeneity in high yield (1 mg/10 mL of culture). The major differences of the E. coli I-1-Pase from all the other characterized I-1-Pases are that it exists as a monomer (rather than a dimer or tetramer) in solution and is more hydrophobic. These physical differences, rather than the I-1-Pase activity, may be involved in the biological role of wild-type SuhB in E. coli.
Disability and quality of life impact of mental disorders in Europe: results from the European Study of the Epidemiology of Mental Disorders (ESEMeD) project (2004)

The results suggest that mental disorders are important determinants of work role disability and quality of life, often outnumbering the impact of common chronic physical disorders.
Pediatric intensive care (1986)

The impact of acute disease, chronic disease, age, and therapeutic goals on resource utilization was evaluated by surveying 397 consecutive admissions to a pediatric ICU. Resource consumption was estimated using ICU days of care and the Therapeutic Intervention Scoring System. Resource consumption was greatest for patients with the therapeutic goal of palliation with hope for definitive repair in the future, patients with acute congenital disease, and children less than one month of age. Significant chronic disease was common (33.5%) but was not associated with increased resource consumption.
Helenalin‐mediated post‐transcriptional regulation of p21(Cip1) inhibits 3T3‐L1 preadipocyte proliferation (2008)

We have previously shown that post-transcriptional mechanisms involving the 26S proteasome regulate the cyclin-dependent kinase inhibitors (CKIs), p21(Cip1) and p27(Kip1) during preadipocyte proliferation. Earlier studies further demonstrated that the anti-inflammatory, anti-carcinogenic phytochemical, helenalin is a potent inhibitor of periodic Skp2 accumulation, an F-box protein mediating SCF E3 ligase ubiquitylation and degradation of both CKIs during S phase progression. Data presented here demonstrate that helenalin dose-dependently induced G1 arrest of synchronously replicating 3T3-L1 preadipocytes. This effect occurred in the absence of discernable indices of cell toxicity or apoptosis under the conditions used in this study. Our results demonstrate that helenalin markedly increased p21 protein accumulation in both density-arrested and proliferating preadipocytes in a dose-dependent manner. This increase in p21 protein abundance occurred without change in mRNA transcript demonstrating that post-transcriptional mechanisms were involved. This notion was further supported by the modest accumulation of polyubiquitylated p21 following treatment with helenalin suggesting that suppression of targeted p21 proteolysis by the 26S proteasome contributed to helenalin-mediated p21 accumulation. The increase in p21 protein was compartmentalized to the nucleus where p21 is known to inhibit cell cycle progression. Finally, helenalin increased protein-protein interactions between p21 and cyclin-dependent kinase 2 (Cdk2) which may account in part for the anti-proliferative effect in 3T3-L1 preadipocytes.
Standardizing <i><scp>CYP</scp>2D6</i> Genotype to Phenotype Translation: Consensus Recommendations from the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group (2019)

Translating CYP2D6 genotype to metabolizer phenotype is not standardized across clinical laboratories offering pharmacogenetic (PGx) testing and PGx clinical practice guidelines, such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). The genotype to phenotype translation discordance between laboratories and guidelines can cause discordant cytochrome P450 2D6 (CYP2D6) phenotype assignments and, thus lead to inconsistent therapeutic recommendations and confusion among patients and clinicians. A modified-Delphi method was used to obtain consensus for a uniform system for translating CYP2D6 genotype to phenotype among a panel of international CYP2D6 experts. Experts with diverse involvement in CYP2D6 interpretation (clinicians, researchers, genetic testing laboratorians, and PGx implementers; n = 37) participated in conference calls and surveys. After completion of 7 surveys, a consensus (> 70%) was reached with 82% of the CYP2D6 experts agreeing to the final CYP2D6 genotype to phenotype translation method. Broad adoption of the proposed CYP2D6 genotype to phenotype translation method by guideline developers, such as CPIC and DPWG, and clinical laboratories as well as researchers will result in more consistent interpretation of CYP2D6 genotype.
Transfection with extracellularly UV-damaged DNA induces human and rat cells to express a mutator phenotype towards parvovirus H-1. (1984)

Human and rat cells transfected with UV-irradiated linear double-stranded DNA from calf thymus displayed a mutator activity. This phenotype was identified by growing a lytic thermosensitive single-stranded DNA virus (parvovirus H-1) in those cells and determining viral reversion frequencies. Likewise, exogenous UV-irradiated closed circular DNAs, either double-stranded (simian virus 40) or single-stranded (phi X174), enhanced the ability of recipient cells to mutate parvovirus H-1. The magnitude of mutator activity expression increased along with the number of UV lesions present in the inoculated DNA up to a saturation level. Unirradiated DNA displayed little inducing capacity, irrespective of whether it was single or double stranded. Deprivation of a functional replication origin did not impede UV-irradiated simian virus 40 DNA from providing rat and human cells with a mutator function. Our data suggest that in mammalian cells a trans-acting mutagenic signal might be generated from UV-irradiated DNA without the necessity for damaged DNA to replicate.
New Well Completion and Stimulation Techniques Using Liquid Jet Cutting Technology (1993)

Abstract Liquid jet cutting technology has made rapid advancement in industries for manufacturing, industrial cleaning and mining. Commonly, pressures from 5000 psi to 60,000 psi are used. In recent years, a number of downhole assemblies have been developed to utilize this technology for use in the oil industry. This paper will cover the development of two such techniques that are capable of creating tunnels in the formation rock up to ten feet in length by one inch in diameter in cased hole or open hole wells. The original design of the downhole assemblies will be discussed. New data on the lab and field testing of the effectiveness of creating tunnels in a variety of formation rocks, jetting with aqueous and acidic fluids will be mentioned. The results will show substantially improved penetration rate when jetting with HCl in carbonate rocks and improved penetration rate when pumping with polymer additives. These techniques provide new options in completing and stimulating zones in a variety of applications. The techniques discussed will provide completion engineers with selective, controlled options for initial completion, stimulation or workover. The resulting tunnels are superior to perforations in length, and diameter and leave no compaction. This paper will also serve to inform the industry of the significance of liquid jet cutting for a variety of downhole applications.
An offset cancellation bit-line sensing scheme for low-voltage DRAM applications (2005)

Offset-cancellation provides low-voltage DRAM operation. The offset cancelling bit-line sense amplifiers are pitch-matched to the conventional 0.16 /spl mu/m DRAM cell array without process modifications. Results indicate better refresh characteristics than conventional bit-line sense amplifiers even at 1.5 V.
Synthesis and Biological Evaluation of a Series of Quinazoline‐2‐carboxylic Acids and Quinazoline‐2,4‐diones as Glycine‐NMDA Antagonists: A Pharmacophore Model Based Approach (1997)

The synthesis and glycine-NMDA binding activity of a series of quinazoline-2-carboxylic acids 1 and quinazoline-2,4-diones 2, containing all the essential and optional pharmacophoric descriptors required by a putative glycine antagonist model, are reported. The binding results show that only three of the title compounds displayed micromolar receptor affinity, demonstrating how disappointing the synthesis of receptor ligands based only on interaction models can be.
SMALL CAST THORIUM OXIDE CRUCIBLES* (1935)

ABSTRACT Crucibles were made from thorium oxide by casting from a slip made according to ceramic practice. The presence of cryolite in the slip insured its successful use. These were fired to 1885°C in a gas furnace of special construction. The addition of zirconium oxide makes a crucible easier to manufacture. The finished crucibles were successfully used in vacuum‐induction furnaces to melt pure metals to 2300°C. No contamination of the metals resulted. Expansion curves indicate a peculiar action of the crucibles made with zirconium oxide in the 700 to 900° region. The mean coefficient of expansion of fused thoria is found to be 93 × from 0 to 600°C. These crucibles are found to be (a) fairly resistant to chemical reagents, but not enough so for chemical work and (b) resistant to wetting of molten metals of high melting point.
The initial ion velocity and its dependence on matrix, analyte and preparation method in ultraviolet matrix-assisted laser desorption/ionization (1999)

Since the early days of matrix-assisted laser desorption/ionization (MALDI), measurements showing that MALDI ions and neutrals have high initial velocities have led to wide acceptance of the idea that a jet of released material entrains analyte ions. The initial velocity, which could previously be determined only with large uncertainty, can be measured today with high reliability in a delayed-extraction MALDI/time-of-flight system by following the linear dependence of ion flight time vs the applied extraction delay. The detection of different initial velocities for different matrices, with and without additives, for various preparation protocols and for different classes of analytes proves that the magnitude of the initial velocity can indeed be regarded as a valuable and meaningful characteristic of the MALDI process. Based on the results reported here, it is postulated that a high initial velocity results from incorporation of the analyte into the matrix crystals and that cooling upon expansion is effective at high initial velocities and responsible for reduced fragmentation observed in such cases compared with ‘slow’ matrices. Copyright © 1999 John Wiley & Sons, Ltd.
Ethics in Organizations: Fundamental Problems, Trivial Applications? (2004)

An organization is made up of people, structures, rules, capital and technology, i.e. tangible and intangible assets whose utilization needs to be coordinated: optimised rationally, in the mind of the economists, influenced by the thoughts and behavior of its members, in the minds of sociologists. In fact both aspects are relevant, especially in business organizations, hence corporate ethics are concerned, linked to governance and “corporate social responsibility” (CSR). These three concepts are object of crucial debates on theoretical and operational levels. Some of the main aspects concerned are presented in the article.
Multiproduct Price Optimization and Competition Under the Nested Logit Model with Product-Differentiated Price Sensitivities (2014)

We study firms that sell multiple substitutable products and customers whose purchase behavior follows a nested logit model, of which the multinomial logit model is a special case. Customers make purchasing decisions sequentially under the nested logit model: they first select a nest of products and subsequently purchase one within the selected nest. We consider the multiproduct pricing problem under the general nested logit model with product-differentiated price sensitivities and arbitrary nest coefficients. We show that the adjusted markup, defined as price minus cost minus the reciprocal of price sensitivity, is constant for all the products within a nest at optimality. This reduces the problem's dimension to a single variable per nest. We also show that the adjusted nest-level markup is nest invariant for all the nests, which further reduces the problem to maximizing a single-variable unimodal function under mild conditions. We also use this result to simplify the oligopolistic multiproduct price competition and characterize the Nash equilibrium. We also consider more general attraction functions that include the linear utility and the multiplicative competitive interaction models as special cases, and we show that similar techniques can be used to significantly simplify the corresponding pricing problems.
Self calibration of Stewart-Gough parallel robots without extra sensors (1999)

Presents a method for the autonomous calibration of six degrees-of-freedom parallel robots. The calibration makes use of the motorized prismatic joint positions corresponding to some sets of configurations where in each set either a passive universal joint or a passive spherical joint is fixed using a lock mechanism. Simulations give us an idea about the number of sets that must be used, the number of configurations by set and the effect of noise on the calibration accuracy. The main advantage of this method is that it can be executed rapidly without need to external sensors to measure the position or the orientation of the mobile platform.
Tumor Secretion of CCL22 Activates Intratumoral Treg Infiltration and Is Independent Prognostic Predictor of Breast Cancer (2013)

It has been reported that dense intratumoral infiltration of Foxp3 (+)Tregs (Tregs) was an independent factor for poor prognosis of breast cancer (BC) patients. However, the cytokines activating the Treg infiltration are not known. This study was undertaken to evaluate the role of CCL22 and TGF-β1 in this cascade and their prognostic significance for BC patients. 417 cases of invasive breast cancer were selected from the prior study cohort and the expressions of CCL22 and TGF-β1 were assessed by immunohistochemistry. It was identified that tumor secretion of CCL22 was positively correlated with the intratumoral Treg infiltration (P<0.0001), but its association with lymphoid aggregates surrounding the tumor was not proven to be significant (P=0.056). Moreover, CCL22 expression was found to be associated with the tumor histological features known to be related with unfavorable prognosis of patients, including high histological grade (P<0.0001), negative ER (P<0.0001), negative PR (P=0.001), and HER2 amplification (P=0.028). Similar to intratumoral Treg infiltrates, CCL22 tumor secretion correlated with the prognosis of the molecular subtypes of breast carcinoma (P<0.0001). Univariate analysis revealed CCL22 to be an independent prognostic factor for overall survival (OS, P<0.0001) and progression-free survival (PFS, P<0.0001) of BC patients that were confirmed by multivariate analysis (P=0.011 and P=0.010 respectively). In contrast, although TGF-β1 expression was positively correlated with both Tregs infiltrates into the tumor bed and lymphoid aggregates surrounding the tumor (P=0.023; P=0.046, respectively), its expression was not significantly associated with the molecular subtypes of breast carcinoma and the prognosis of the patients. Our study indicates that both CCL22 and TGF-β1 are candidate chemoattractants for intratumoral Foxp3 (+)Tregs infiltration; however, unlike the later, CCL22 is an independent prognostic predictor of BC patients, and it therefore may have the potential to serve as a target for immunotherapeutic strategy of BC.
Inferring dynamics from the wavenumber spectra of an eddying global ocean model with embedded tides (2012)

The slopes of the wavenumber spectra of sea surface height (SSH) and kinetic energy (KE) have been used to infer “interior” or surface quasi‐geostrophic (QG or SQG) dynamics of the ocean. However, inspection of spectral slopes for altimeter SSH in the mesoscale band of 70 to 250 km shows much flatter slopes than the QG or SQG predictions over most of the ocean. Comparison of altimeter wavenumber spectra with spectra from an eddy resolving global ocean circulation model (the HYbrid Coordinate Ocean Model, HYCOM, at 1/12.5° equatorial resolution), which has embedded tides, suggests that the flatter slopes of the altimeter SSH may arise from three possible sources: (1) presence of strong internal tides, (2) shift of the inertial sub‐range to smaller scales and (3) altimeter noise. Artificially adding noise to the model tends to flatten the spectra for low KE regions. Near internal tide generating regions, spectral slopes in the presence of internal waves are much flatter than QG or SQG predictions. Separating the variability into high and low frequency (around periods of 2 days), then a different pattern emerges with a flat high‐frequency wavenumber spectrum and a steeper low‐frequency wavenumber spectrum. For low mesoscale KE, the inertial sub‐range, defined by the nearly flat enstrophy band, moves to smaller scales and the mesoscale band of 70 to 250 km no longer represents the inertial sub‐range. The model wavenumber spectra are consistent with QG and SQG theory when internal waves and inertial sub‐range shifts are taken into consideration.
Overhead and Performance Study of the General Internet Signaling Transport (GIST) Protocol (2006)

The General Internet Signaling Transport (GIST) protocol is currently being developed as the base protocol compo-nent in the IETF Next Steps In Signaling (NSIS) protocol stack to support a variety of signaling applications. We present our study on the protocol overhead and performance aspects of GIST. We quantify network-layer protocol overhead and observe the effects of enhanced modularity and security in GIST. We developed a first open source GIST implementation at the University of Gottingen, and study its performance in a Linux testbed. A GIST node serving 45 000 signaling sessions is found to consume average only 1.1 ms for processing a signaling message and 2.4 KB of memory for managing a session. Individual routines in the GIST code are instrumented to obtain a detailed profile of their contributions to the overall system processing. Important factors in determining performance, such as the number of sessions, state management, refresh frequency, timer management and signaling message size are further discussed. We investigate several mechanisms to improve GIST performance so that it is comparable to an RSVP implementation.
Can Uhear me now? Validation of an iPod-based hearing loss screening test. (2012)

The uHear application is a reasonable screening test to rule out moderate hearing loss (PTA > 40 dB) and and is valid at quantifying the degree of hearing loss in patients known to have abnormal hearing.
Steroid regulation of terminal protein glycosyltransferase genes: molecular and functional homologies within sialyltransferase and fucosyltransferase families. (2003)

Terminal glycosylations such as fucosylation and especially sialylation are crucial in maturation of proteins for their particular function. In cells and tissues where their function is under hormonal control, often terminal processes including glycosylations are tightly regulated by hormones. Therefore, it is not surprising that two key enzyme families involved in these steps, fucosyltransferases and sialyltransferases, are directly controlled by steroid hormones.Gene structure and protein sequences have been analyzed by set of Unix-based complex sequence analysis programs of the Wisconsin GCG package, and from some other resources. Protein secondary structure predictions were based on several independent programs and applications complementing each other depending on the algorithm used, all running on Unix platforms.Comparison of these two types of enzymes from organisms where they are known to be under direct hormonal regulation has revealed that although sialyltransferases are broad family of proteins, the only known enzymes to be under hormonal control are alpha-2,6-sialyltransferases and in the case of fucosyl moieties transferring enzymes these are alpha-1,2/6-fucosyltransferases. Interestingly, hormonally regulated sialyltransferases from as evolutionary distant organisms as human and fruitfly share several important features including secondary structure characteristics encompassing sialyl L and S motifs in which they differ from other sialyltransferases. Analogous organizational and structural similarities were found also in hormonally regulated fucosyltransferases.Data indicate that hormonal control of these classes of enzymes as a regulatory mechanism could be attained relatively early during the evolution in order to obtain selective control over specific protein modification process which plays an important role during ontogenic development.
Frequency of major pediatric illnesses hospitalized in Taiwan. (1994)

From January 1987 to December 1989, there were a total of 158,576 pediatric admissions to 24 major hospitals in Taiwan. The most common diseases leading to admission included respiratory tract disease (28.88%), neonatal illness (18.44%), gastrointestinal tract disease (14.20%) and common infectious diseases (8.45%). More than half (58.8%) of the children with respiratory tract disease had bronchopneumonia, and 80.8% of the children with gastrointestinal tract disease suffered from diarrhea. During the three-year study period, the average number of children under 14 years of age in Taiwan was 5,556,839. The frequency of each major illness per 1,000 children-years was thus 2.75 for respiratory tract disease, 1.75 for neonatal illness, 1.35 for gastrointestinal tract disease, 0.84 for common infectious disease, 0.49 for cardiovascular disease, 0.38 for neurological disorders, 0.27 for allergic diseases, 0.27 for hemato-oncologic disease, 0.14 for accidents, 0.13 for renal disease and 0.02 for metabolic disease.