gebhart/patrepeval huggingface dataset:
Stable inheritance of plasmid R1 requires two different loci (1985)

The largest EcoRI fragment from plasmid R1 mediates a stability phenotype which is required to ensure the stable inheritance of this low-copy-number plasmid. When covalently linked to small, unstable R1 derivatives, this fragment makes the plasmids as stable as the wild-type R1 plasmid. A genetic analysis showed that two independently acting stabilization functions are encoded by this EcoRI fragment, both of which have the potential of partial stabilization of mini-R1 plasmids. The two loci are located at opposite ends of the fragment. Stabilization was also obtained by inserting these regions in unrelated, unstable plasmids from the p15 group. One of the two functions was very efficient in stabilizing such foreign replicons. Besides the stability phenotype, these genes exert incompatibility in an allele-specific manner. The stability functions do not seem to interfere seriously with the copy number of the plasmid.
A 250-622 MHz deskew and jitter-suppressed clock buffer using two-loop architecture (1996)

A 250-622 MHz clock buffer has been developed, using a two-loop architecture: a delay-locked loop (DLL) for deskew, and a frequency-locked loop (FLL) for reference frequency supply to the DLL. The DLL incorporates a current-mode phase detector which utilizes a flip-flop metastability to detect a phase difference in the order of 20 ps. A measured jitter is suppressed to less than 40 ps RMS over the operating frequency range. A DLL acquisition time of 150 ns typical is simulated at 400 MHz. A 0.4-/spl mu/m CMOS technology is used to fabricate the chip.
Metabolism of 2',2'-difluoro-2'-deoxycytidine and radiation sensitization of human colon carcinoma cells. (1994)

Difluorodeoxycytidine (dFdCyd) is a new antimetabolite with clinical activity in patients with solid tumors but not leukemias. We have studied the metabolism, cytotoxicity, and radiosensitizing properties of dFdCyd in HT-29 human colon carcinoma cells. The results demonstrated that dFdCyd rapidly accumulated as the 5'-triphosphate dFdCTP in HT-29 cells, which was eliminated slowly in the absence of dFdCyd with a half-life of > 12 h. Accumulation of dFdCTP was associated with rapid depletion of cellular dATP pools. Exposure to the concentration that reduces cell survival by 50% of 30 nM dFdCyd decreased dATP levels by > 80% within 4 h. dGTP pools were depleted at higher concentrations of dFdCyd, whereas smaller decreases were effected in dTTP and dCTP pools. These results contrast with previous reports in leukemic cells which demonstrated that dFdCyd exposure depleted the endogenous dCTP pool to a greater extent than the dTTP, dATP, or dGTP pools. Based on these data, we suggest that the profound depletion by dFdCyd of dATP and dGTP pools in HT-29 compared to leukemic cells accounts for the superiority of this agent in solid tumors versus leukemias. Additional studies demonstrated that dFdCyd was a potent radiosensitizer in HT-29 cells. Maximal radiosensitization was observed when cells were irradiated immediately following dFdCyd exposure instead of prior to or in the middle of drug treatment. Radiation sensitization was dose and time dependent, with a noncytotoxic exposure to 10 nM dFdCyd for 24 h or 30 nM dFdCyd for 16 h producing a radiation enhancement ratio of approximately 2. Under these conditions, only the cellular dATP pool was depleted. When cells were exposed to higher concentrations of dFdCyd for 4 h, equivalent radiosensitization with a radiation enhancement ratio of 1.4 was obtained using 0.1, 1.0, or 10 microM dFdCyd. Despite a 15-fold increase in dFdCTP and depletion of dGTP and dCTP pools to < 25% of the control value with 10 microM compared to 0.1 microM dFdCyd, no increase in radiosensitization was observed. These results suggest that dATP depletion is an important factor in the radiosensitizing property of this promising new antitumor compound.
Channel estimation and prediction for adaptive OFDM downlinks [vehicular applications] (2003)

Channel estimation and prediction algorithms are developed and evaluated for use in broadband adaptive OFDM downlinks over fading channels for vehicular users. Accurate channel estimation may be obtained by using a combined pilot-aided and decision-directed approach based on Kalman filtering and prediction. The correlation properties of the channel in both time and space are taken into account. Kalman performance at much lower computational complexity is attained with recently developed constant gain adaptation laws. We present and evaluate a state-space realization of such an adaptation law, with computational complexity of the order of the square of the number of parallel tracked pilot subcarriers. In an adaptive OFDM system, prediction of the channel power a few milliseconds ahead are also required. Frequency-domain channel estimates can be transformed to the time domain, and used as regressors in channel predictors based on linear regression. We also make a preliminary evaluation of the direct use of complex channel prediction in the frequency domain for channel power prediction.
Development of Improved Chemicals and Plastics from Oilseeds (2006)

The overall objective of this program was to develop technology that can be applied to the production of various chemicals and plastics from seed oils. This research and development program included activities in all four key barrier areas identified in the US DOE Technology Roadmap for Plant/Crop-Based Renewable Resources, namely Plant Science, Production, Processing, and Utilization. Participants in the project included The Dow Chemical Company, Castor Oil, Inc., and the USDA Western Regional Research Center (WRRC). The objective of this production task was to evaluate and develop metathesis catalyst technology as a means of utilizing seed oils as feedstocks for the chemical industry. Specifically, ethenolysis of fatty acid methyl esters, FAME’s, leads to functionalized derivatives. These serve as valuable starting points for materials which cascade into a variety of applications, many of which have a current market presence. The relatively recent discovery and commercial availability of a family of metathesis catalysts which are tolerant of polar functional groups and the acquisition and implementation of high throughput synthesis and screening infrastructure led to a prime opportunity to investigate this project area.
Effects of Surface-Modified Alkyl Chain Length of Silica Fillers on the Rheological and Thermal Mechanical Properties of Underfill (2016)

Due to the increased packaging density as well as the size reduction of the gap between the chip and the substrate in modern flip-chip technology, there is an increasing demand for the use of nanosized silica particles as fillers into underfill to further improve its comprehensive performance. However, silica nanoparticles (SNPs) cannot uniformly disperse into the polymer matrix and usually cause some negative issues, such as a dramatic increase in viscosity and a significant decrease in the glass transition temperature as a result of their excessive surface energy and surface hydrophilic silanol groups. Surface modification with alkyl chains is an effective way to facilitate a uniform dispersion of nanofillers in polymer matrix since suitable repulsive forces can optimize spacing among nanoparticles by decreasing interactions between nanoparticles and changing the surface property of nanoparticles from hydrophilic to hydrophobic. In this paper, SNPs surface-modified by alkyl groups of different lengths were prepared and used as fillers to study the role of the surface alkyl chain length in the rheological and thermal-mechanical properties of underfill nanocomposites. It was found that surface alkyl chains could improve the dispersion of SNPs in epoxy matrix, and thus contributed to decrease the viscosity and enhance the glass transition temperature of underfill nanocomposites. With an increase in the surface alkyl chain length, the viscosity of underfill nanocomposites increased and the glass transition temperature shifted to a higher temperature. This paper sets the way toward the choice of an alkyl chain of proper length as filler surface functional group to improve the comprehensive performance of underfill.
Peripheral Blood CD161+ T Cells from Asthmatic Patients are Activated During Asthma Attack and Predominantly Produce IFN‐γ (2007)

In humans, T cells expressing the CD161 molecule NKR-P1A constitute around 20% of the circulating CD3(+) cells and are potentially immunoregulatory in several diseases. Their role in asthma is not well known, but they could participate in asthma attacks. To determinate whether activation of CD161(+) T cells and their cytokine production correlate with clinical status of asthma, we analysed blood samples from asthma attack patients (AAP) and stable asthma patients (SAP) in comparison with healthy non-atopic controls (HC). There was a significant higher baseline expression of CD69 on T cells from AAP and the difference was more notorious on CD161(+) T cells; upregulation of CD69 was observed on both CD161(-) and CD161(+) T cells driven by Dermatophagoides pteronyssinus crude extract, whereas polyclonal stimulation with phorbol 12-myristate 13-acetate plus ionomycin predominantly induced IFN-gamma but no IL-4, IL-5 and IL-13 by CD161(+) T cells in all groups; upon polyclonal stimulation, there were more CD161(+) T cells producing IFN-gamma and less CD161(-) T cells producing this cytokine, contrasting with the opposite results observed in SAP and HC groups. Our results indicate that, during asthma attack, CD161(+) T cells are activated and are able to produce predominantly IFN-gamma but no Th2 cytokines. We hypothesize that during an asthma attack, IFN-gamma produced by CD161(+) T cells could help to reestablish the Th1/Th2 equilibrium. These observations may contribute to the understanding of the immune mechanisms involved in asthma attacks.
Efficient production of active TNF‐α by albumin signal peptide (1997)

TNF-alpha is initially synthesized as a membrane-anchored precursor protein and processed proteolytically by a matrix metalloproteinase (MMP)-like enzyme. In order to establish an efficient expression system of TNF-alpha in mammalian cells without involvement of the extracellular enzyme, an expression plasmid (pCN-alb-TNF) was constructed with a signal sequence of the rat albumin gene as a module for secretion. The highest level of production of TNF-alpha was observed in the clone CT-3 by SDS-PAGE and Western blot analysis. Biological activity of the secretion was revealed by repression of catalase gene expression in hepatoma cells and cytotoxity to L929 cells. Attachment of the signal peptide to mature form resulted in the enhancement of production of the cytokine.
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors (1993)

We present a systematic analysis of sequence motifs found in metazoan protein factors involved in constitutive pre-mRNA splicing and in alternative splicing regulation. Using profile analysis we constructed a database enriched in protein sequences containing one or more presumptive copies of the RNA-recognition motif (RRM). We provide an accurate alignment of RRMs and structure-based criteria for identifying new RRMs, including many that lack the prototype RNP-1 submotif. We present a comprehensive table of 125 sequences containing 252 RRMs, including 22 previously unreported RRMs in 17 proteins. The presence of a putative RRM in these proteins, which are implicated in a variety of cellular processes, strongly suggests that their function involves binding to RNA. Unreported homologies in the RRM-enriched database to the metazoan SR family of splicing factors are described for an Arg-rich human nuclear protein and two yeast proteins (S. pombe mei2 and S. cerevisiae Npl3). We have rigorously tested the phylogenetic relationships of a large sample of RRMs. This analysis indicates that the RRM is an ancient conserved region (ACR) that has diversified by duplication of genes and intragenic domains. Statistical analyses and classification of repeated Arg-Ser (RS) and RGG domains in various protein splicing factors are presented.
Secure Coprocessor Integration with Kerberos V5 (2000)

As a developing country, the economic and population growth rates in Ghana over the past few years have seen a tremendous increase. The growing rate of industrialization is gradually leading to contamination and deterioration of the environment and pollution is likely to reach disturbing levels. Surface soil samples were collected randomly from 36 communities in the Kumasi Metropolis, Ghana, to determine the concentrations, distribution, sources and toxic potential of emission of polycyclic aromatic hydrocarbons (PAHs) since no such comprehensive study had been conducted. The mean concentration of total PAHs in the surface soils in each community ranged from 14.78 at Ahinsan to 2084 ng/g dry weight at Adum with an average of 442.5 ± 527.2 ng/g dry weight. Diagnostic ratios and chemical mass balance models of the results showed that PAHs in surface soil samples from the study area were mainly from fuel combustion. Carcinogenic potency of PAH load from the city centre was approximately 150 times higher as compared to a pristine site, Kwame Nkrumah University of Science and Technology's Botanical Garden. BaP, a human carcinogen, contributed 70% of the total PAHs toxicity level from the city centre of Kumasi.
Salicylic acid 3-hydroxylase regulates Arabidopsis leaf longevity by mediating salicylic acid catabolism (2013)

The plant hormone salicylic acid (SA) plays critical roles in plant defense, stress responses, and senescence. Although SA biosynthesis is well understood, the pathways by which SA is catabolized remain elusive. Here we report the identification and characterization of an SA 3-hydroxylase (S3H) involved in SA catabolism during leaf senescence. S3H is associated with senescence and is inducible by SA and is thus a key part of a negative feedback regulation system of SA levels during senescence. The enzyme converts SA (with a Km of 58.29 µM) to both 2,3-dihydroxybenzoic acid (2,3-DHBA) and 2,5-DHBA in vitro but only 2,3-DHBA in vivo. The s3h knockout mutants fail to produce 2,3-DHBA sugar conjugates, accumulate very high levels of SA and its sugar conjugates, and exhibit a precocious senescence phenotype. Conversely, the gain-of-function lines contain high levels of 2,3-DHBA sugar conjugates and extremely low levels of SA and its sugar conjugates and display a significantly extended leaf longevity. This research reveals an elegant SA catabolic mechanism by which plants regulate SA levels by converting it to 2,3-DHBA to prevent SA overaccumulation. The research also provides strong molecular genetic evidence for an important role of SA in regulating the onset and rate of leaf senescence.
COP1 enhances ubiquitin-mediated degradation of p27Kip1 to promote cancer cell growth (2015)

p27 is a critical CDK inhibitor involved in cell cycle regulation, and its stability is critical for cell proliferation. Constitutive photomorphogenic 1 (COP1) is a RING-containing E3 ubiquitin ligase involved in regulating important target proteins for cell growth, but its biological activity in cell cycle progression is not well characterized. Here, we report that p27Kip1 levels are accumulated in G1 phase, with concurrent reduction of COP1 levels. Mechanistic studies show that COP1 directly interacts with p27 through a VP motif on p27 and functions as an E3 ligase of p27 to accelerate the ubiquitin-mediated degradation of p27. Also, COP1-p27 axis deregulation is involved in tumorigenesis. These findings define a new mechanism for posttranslational regulation of p27 and provide insight into the characteristics of COP1-overexpressing cancers.
Identification of chronic hepatitis C patients without hepatic fibrosis by a simple predictive model (2002)

Liver biopsy is required for staging hepatic fibrosis in patients with chronic hepatitis C, but it is an expensive procedure with occasional complications and poor patient acceptance. This cohort study was designed to assess the accuracy of a noninvasive method aimed to discriminate between patients with and without significant liver fibrosis (stages 2-4 versus 0-1). Clinically relevant variables were analyzed in a cohort of 476 consecutive untreated patients (estimation group, 351 patients; validation group, 125 patients) with chronic hepatitis C who underwent a liver biopsy. Multivariate analysis identified age, gamma glutamyl transpeptidase (GGT), cholesterol, platelet count, and prothrombin time as independent predictors of fibrosis. We constructed a model and a score system combining age, GGT, cholesterol, and platelet count that proved useful to identify patients without significant hepatic fibrosis. The area under the ROC curve was 0.86 for the estimation group and 0.81 for the validation group. Using the best cutoff score (less than 4.2), presence of significant fibrosis (F2 to F4) could be excluded with high accuracy (negative predictive value of 96%) in 125 (36%) of 351 patients. Similarly, it could be excluded with the same certainty in 49 (39%) of the 125 patients of the validation group. Only 2 patients with liver fibrosis stage 2 were incorrectly classified. In conclusion, a combination of easily accessible variables accurately predicts the absence of significant fibrosis and might render liver biopsy unnecessary in more than one third of patients with chronic hepatitis C.
Group-based motivational interviewing for alcohol use among college students: An exploratory study. (2006)

How can practicing psychologists help reduce excessive alcohol consumption among college students? Over 80% of college students consume alcohol, and a significant percentage drinks excessively with myriad problems. Brief interventions based on motivational interviewing (MI) have been identified for use with college populations. The authors randomly assigned 91 freshman students to a brief, classroom-based MI intervention or an assessment control condition. At the end of the semester, MI group participants reported fewer drinks per occasion and fewer episodes of intoxication compared to controls. A classroom-based, MI-style intervention might be an efficient, sustainable, and effective means of reducing heavy drinking among college students.
Migraine and its psychiatric comorbidities (2016)

Migraine is a highly prevalent and disabling neurological disorder associated with a wide range of psychiatric comorbidities. In this manuscript, we provide an overview of the link between migraine and several comorbid psychiatric disorders, including depression, anxiety and post-traumatic stress disorder. We present data on psychiatric risk factors for migraine chronification. We discuss the evidence, theories and methods, such as brain functional imaging, to explain the pathophysiological links between migraine and psychiatric disorders. Finally, we provide an overview of the treatment considerations for treating migraine with psychiatric comorbidities. In conclusion, a review of the literature demonstrates the wide variety of psychiatric comorbidities with migraine. However, more research is needed to elucidate the neurocircuitry underlying the association between migraine and the comorbid psychiatric conditions and to determine the most effective treatment for migraine with psychiatric comorbidity.
An overview of the c-MET signaling pathway (2011)

c-MET is a receptor tyrosine kinase that, after binding with its ligand, hepatocyte growth factor, activates a wide range of different cellular signaling pathways, including those involved in proliferation, motility, migration and invasion. Although c-MET is important in the control of tissue homeostasis under normal physiological conditions, it has also been found to be aberrantly activated in human cancers via mutation, amplification or protein overexpression. This paper provides an overview of the c-MET signaling pathway, including its role in the development of cancers, and provides a rationale for targeting the pathway as a possible treatment option.
Conservative treatment of plantar fasciitis. A prospective study (1998)

A randomized, prospective study was conducted to compare the individual effectiveness of three types of conservative therapy in the treatment of plantar fasciitis. One hundred three subjects were randomly assigned to one of three treatment categories: anti-inflammatory, accommodative, or mechanical. Subjects were treated for 3 months, with follow-up visits at 2, 4, 6, and 12 weeks. For the 85 patients who completed the study, a statistically significant difference was noted between groups, with mechanical treatment with taping and orthoses proving to be more effective than either anti-inflammatory or accommodative modalities.
Metabolism of Melamine by Klebsiella terragena (1997)

Experiments were conducted to determine the pathway of melamine metabolism by Klebsiella terragena (strain DRS-1) and the effect of added NH(inf4)(sup+) on the rates and extent of melamine metabolism. In the absence of added NH(inf4)(sup+), 1 mM melamine was metabolized concomitantly with growth. Ammeline, ammelide, cyanuric acid, and NH(inf4)(sup+) accumulated transiently in the culture medium to maximal concentrations of 0.012 mM, 0.39 mM, trace levels, and 0.61 mM, respectively. In separate incubations, in which cells were grown on either ammeline or ammelide (in the absence of NH(inf4)(sup+)), ammeline was metabolized without a lag while ammelide metabolism was observed only after 3 h. In the presence of 6 mM added NH(inf4)(sup+) (enriched with 5% (sup15)N), ammeline, ammelide, and cyanuric acid accumulated transiently to maximal concentrations of 0.002 mM, 0.47 mM, and trace levels, respectively, indicating that the added NH(inf4)(sup+) had little effect on the relative rates of triazine metabolism. These data suggest that the primary mode of melamine metabolism by K. terragena is hydrolytic, resulting in successive deaminations of the triazine ring. Use of (sup15)N-enriched NH(inf4)(sup+) allowed estimates of rates of triazine-N mineralization and assimilation of NH(inf4)(sup+)-N versus triazine-N into biomass. A decrease in the percent (sup15)N in the external NH(inf4)(sup+) pool, in conjunction with the accumulation of ammelide and/or triazine-derived NH(inf4)(sup+) in the culture medium, suggests that the initial reactions in the melamine metabolic pathway may occur outside the cytoplasmic membrane.
Formal semantics and verification for feature modeling (2005)

Research on features has received much attention in the domain engineering community. Feature modeling plays an important role in the design and implementation of complex software systems. However, the presentation and analysis of feature models are still largely informal. There is also an increasing need for methods and tools that can support automated feature model analysis. This paper presents a formal engineering approach to the specification and verification of feature models. A formal semantics for the feature modeling language is defined using first-order logic. It provides a precise and rigorous formal interpretation for the graphical notation. In addition, further validation of the semantics using the Z/EVES theorem prover is presented. Finally, we demonstrate that the consistency of a feature model and its configurations can be automatically verified by encoding the semantics into the Alloy Analyzer. A case study of the Key Word in Context (KWIC) index systems feature model is presented to illustrate the verification process.