gebhart/patrepeval huggingface dataset:
The Making of a Slicer: Activation of Human Argonaute-1 (2013)

Argonautes are the central protein component in small RNA silencing pathways. Of the four human Argonautes (hAgo1-hAgo4) only hAgo2 is an active slicer. We determined the structure of hAgo1 bound to endogenous copurified RNAs to 1.75 Å resolution and hAgo1 loaded with let-7 microRNA to 2.1 Å. Both structures are strikingly similar to the structures of hAgo2. A conserved catalytic tetrad within the PIWI domain of hAgo2 is required for its slicing activity. Completion of the tetrad, combined with a mutation on a loop adjacent to the active site of hAgo1, results in slicer activity that is substantially enhanced by swapping in the N domain of hAgo2. hAgo3, with an intact tetrad, becomes an active slicer by swapping the N domain of hAgo2 without additional mutations. Intriguingly, the elements that make Argonaute an active slicer involve a sophisticated interplay between the active site and more distant regions of the enzyme.
Orientation of liquid crystals by surface coupling agents (1973)

Uniformly oriented thin liquid-crystal layers are required for most liquid-crystal device applications and physical investigations. Usual methods for obtaining orientation rely on a substrate interface which has an orienting action on the liquid-crystal molecules. In previously described methods the orienting interfaces degrade chemically with time, thereby generating a corresponding degradation of the liquid-crystal orientation. In the present work, silane surface coupling agents are used to obtain chemically stable interfaces and a wide variety of liquid-crystal orientations.
Operational profiles in software-reliability engineering (1993)

A systematic approach to organizing the process of determining the operational profile for guiding software development is presented. The operational profile is a quantitative characterization of how a system will be used that shows how to increase productivity and reliability and speed development by allocating development resources to function on the basis of use. Using an operational profile to guide testing ensures that if testing is terminated and the software is shipped because of schedule constraints, the most-used operations will have received the most testing and the reliability level will be the maximum that is practically achievable for the given test time. For guiding regression testing, it efficiently allocates test cases in accordance with use, so the faults most likely to be found, of those introduced by changes, are the ones that have the most effect on reliability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Clinical Trial of a Chest-Pain Observation Unit for Patients with Unstable Angina (1998)

A CPU located in the emergency department can be a safe, effective, and cost-saving means of ensuring that patients with unstable angina who are considered to be at intermediate risk of cardiovascular events receive appropriate care.
Clustering search results of non-text user generated content (2010)

Non-text user generated content (UGC), such as videos and images, is usually searched by metadata. Metadata, such as title, tags, and description, is created by users whenever content is uploaded. However, in many cases metadata can have multiple meanings. This requires users to spend time sifting through a long list of search results until they can find all the content for which they were actually looking. In order to address this limitation, we suggest an algorithm to cluster search results using keyword similarity. Clustering search results from YouTube are accomplished by using the Markov clustering algorithm, which helps users to quickly and easily find what they want. Finally, we conclude by evaluating the performance results of our clustering algorithm.
A study of data compression using neural networks and principal component analysis (of pulmonary scintigrams) (1989)

PCA analysis is similar to neural networks in data compression of segments that have been 'seen', but is superior in compressing 'unseen' images. The difference between 'seen' and 'unseen' images with respect to tsse (total sum square error) is more pronounced in 32 by 16 pixel segments than 8 by 8 segments in PCA compression. This suggests that the dimensional reduction is more consistent in the smaller segments. However the tsse is lower for 'seen' segments in the larger segment PCs. Artificial neural networks also seem to generalise less readily on larger segments. Since the time taken for neural network compression is about an order of magnitude higher than PCA, and PCA is more repeatable in terms of the error magnitude, and produces lower error for 'unseen' segments, it would seem preferable to use PCA analysis than neural network methods to produce the reduced dimensional input to a diagnostic network.
Characterization of Late-Onset Citrullinemia 1 in a Korean Patient: Confirmation by Argininosuccinate Synthetase Gene Mutation Analysis (2006)

A 16-month old boy was referred to our hospital for evaluation of recurrent generalized tonic clonic seizures. Metabolic evaluation revealed significant hyperammonemia (1,112 microg/dl). Amino acid/acylcarnitine screening using tandem mass spectrometry showed markedly increased plasma levels of citrulline (1,350 microM/l) with undetectable levels of arginine and arginosuccinic acid. Urinary excretion of citrulline was markedly increased (38,617 microM/g creatinine). Brain MRI findings showed diffuse high-signal intensity lesions, that involved gray and white matter in both frontal lobes and insula with edematous changes; these findings were consistent with the acute stage of citrullinemia (CTLN). Mutation analysis of the argininosuccinate synthetase (ASS) gene, in this patient, showed a Gly324Ser mutation in exon 13, and a 67-bp duplication mutation in exon 15 (c.1128-6_1188dup67). The patient was confirmed as having late-onset CTLN1 and treated with anticonvulsants, lactulose enema, protein restricted diet and arginine. Here we describe a case of late-onset CTLN1 in a patient by biochemical analyses and ASS gene mutation confirmation. This is the first report of a Korean patient with late-onset CTLN1 confirmed by ASS gene mutation identification.
Measurement of thermal diffusion in thin films using a modulated laser technique: Application to chemical-vapor-deposited diamond films (1992)

A method to determine the thermal diffusivity in thin films, based on the measurement and analysis of thermal waves induced by a modulated infrared laser, is demonstrated. A nearly exact mathematical description, independent of the film geometry and including surface heat losses, is presented. It is shown that the in-plane thermal diffusivity and the heat loss through the surface can be determined independently by analysis of both the phase and the amplitude of the thermal waves. The validity of the method has been verified using high-purity copper sheets of varying thickness, for different modulation frequencies. Several polycrystalline, chemical-vapor-deposited (CVD) diamond films have been investigated. The measurements were performed both on free-standing films and on two-layer systems of CVD diamond and copper. Thermal diffusivities for polycrystalline diamond up to 6.2 cm2 s−1 were recorded.
Effect of heme arginate administration on blood pressure in spontaneously hypertensive rats. (1990)

Cytochrome P450 content and activities are increased in the kidneys of spontaneously hypertensive rats (SHR) as compared with those of normotensive, Wistar-Kyoto (WKY), control rats during the period of rapid elevation of blood pressure. We studied the effect of heme arginate, a potent inducer of heme oxygenase (EC 1.14.99.3), on microsomal cytochrome P450 levels and activities and blood pressure in SHR at 7 wk of age. Administration of heme arginate (15 mg/kg body weight for 4 d) resulted in a marked decrease in blood pressure from 156.3 +/- 4.7 to 129.8 +/- 4.5 mm Hg (P less than 0.001), whereas blood pressure in SHR receiving the vehicle control was not affected. The blood pressure of age-matched WKY was not affected by heme arginate. Heme oxygenase activity increased in both hepatic and renal microsomes of SHR and WKY by two- to four-fold after treatment with heme arginate. Maximal increase of heme oxygenase mRNA occurred 5-7 h after the last injection of heme arginate and returned to control levels after 24 h. The increase in heme oxygenase activity was associated with a parallel decrease in cytochrome P450 content and in the activity of cytochrome P450 omega/omega-1 arachidonate hydroxylases in kidneys of SHR. It is postulated that heme arginate treatment resulted in induction of heme oxygenase which consequently led to a diminution of cytochrome P450, especially the arachidonate omega/omega-1 hydroxylases leading to a marked decrease in 19-hydroxyeicosatetraenoic acid (HETE) and 20-HETE. The effect of heme arginate on blood pressure may be mediated via these biochemical events inasmuch as both 19-HETE and 20-HETE produced by the kidney may promote hypertension by causing vasoconstriction and sodium retention.
Expression of Mucin Synthesis and Secretion in Human Tracheobronchial Epithelial Cells Grown in Culture (1990)

The effects of culture conditions on growth and differentiation of human tracheobronchial epithelial (HTBE) cells have been defined. Epithelial cells were dissociated from tissues by protease treatment and were plated on tissue culture dishes in F12 medium supplemented with insulin, transferrin, epidermal growth factor, hydrocortisone, cholera toxin, bovine hypothalamus extract, and retinol. HTBE cells did not express any mucociliary function (ciliogenesis or mucin secretion) on tissue culture plastic, but they could be passaged 3 to 5 times with a total of 10 to 25 population doublings. Cells from early passages re-express both these functions when transplanted to tracheal grafts. When tissue culture plates were coated with collagen film or collagen gel substrata, cell attachment and proliferation were stimulated. However, the expression of mucous cell function in culture occurred only when cells were plated on collagen gel substrata and vitamin A (retinol) was present in the medium. Mucous cell differentiation under optimal conditions was defined by ultrastructural studies, by immunologic studies with mucin-specific monoclonal antibodies, and by carbohydrate and amino acid compositional analyses of mucin-like glycoproteins purified from culture medium. These results demonstrate for the first time that HTBE cells can express mucin synthesis and secretion under appropriate culture conditions.
A randomized controlled trial of emotionally expressive writing for women with metastatic breast cancer. (2010)

Although there was no main effect of expressive writing on health among the current metastatic breast cancer sample, expressive writing may be beneficial for a subset of metastatic patients (including women with low levels of emotional support or who have been recently diagnosed) and contraindicated for others (i.e., those who have been living with the diagnosis for years).
Path planning and Ground Control Station simulator for UAV (2013)

In this paper we present a Universal and Interoperable Ground Control Station (UIGCS) simulator for fixed and rotary wing Unmanned Aerial Vehicles (UAVs), and all types of payloads. One of the major constraints is to operate and manage multiple legacy and future UAVs, taking into account the compliance with NATO Combined/Joint Services Operational Environment (STANAG 4586). Another purpose of the station is to assign the UAV a certain degree of autonomy, via autonomous planification/replanification strategies. The paper is organized as follows.
A bacterial process for selenium nanosphere assembly (2011)

During selenate respiration by Thauera selenatis, the reduction of selenate results in the formation of intracellular selenium (Se) deposits that are ultimately secreted as Se nanospheres of approximately 150 nm in diameter. We report that the Se nanospheres are associated with a protein of approximately 95 kDa. Subsequent experiments to investigate the expression and secretion profile of this protein have demonstrated that it is up-regulated and secreted in response to increasing selenite concentrations. The protein was purified from Se nanospheres, and peptide fragments from a tryptic digest were used to identify the gene in the draft T. selenatis genome. A matched open reading frame was located, encoding a protein with a calculated mass of 94.5 kDa. N-terminal sequence analysis of the mature protein revealed no cleavable signal peptide, suggesting that the protein is exported directly from the cytoplasm. The protein has been called Se factor A (SefA), and homologues of known function have not been reported previously. The sefA gene was cloned and expressed in Escherichia coli, and the recombinant His-tagged SefA purified. In vivo experiments demonstrate that SefA forms larger (approximately 300 nm) Se nanospheres in E. coli when treated with selenite, and these are retained within the cell. In vitro assays demonstrate that the formation of Se nanospheres upon the reduction of selenite by glutathione are stabilized by the presence of SefA. The role of SefA in selenium nanosphere assembly has potential for exploitation in bionanomaterial fabrication.
A fast algorithm for color image quantization using only 256 colors (1988)

Abstract In the recent workstation for CAD and CG, a color map display is often used, which can display 256 colors selected from 2 24 (approx. 16000000) colors using a look‐up table. Even in the computer system with such a color display with such a limited number of colors, it is desired that the continuous color image should be processed. In most cases, by determining colors which are important to the image (representative colors), the color image can approximately be displayed without much degrading the image quality. This paper proposes a new method for the approximate display of the color image by 256 colors. In the method, RGB color space is successively partitioned to determine 256 representative colors, so that the quasi‐optimum solution is obtained in the sense of the least‐mean‐square error. By the proposed method, a highly accurate approximate image is obtained with several times faster speed, compared with the traditional methods. The work memory required in the program is only 100 to 200 kBytes, which is less than in the traditional method.
Cysteine‐rich outer membrane proteins of <i>Chlamydia trachomatis</i> display compensatory sequence changes between biovariants (1990)

Two cysteine-rich proteins of Chlamydia trachomatis are essential structural components of the unique outer membrane of the infectious elementary body. These 58,000 (outer membrane protein 2; OMP2) and 15,000 (OMP3) proteins also differ structurally and chemically between biovariants that differ in invasive capability. We have identified the gene for OMP3 and sequenced both trachoma and lymphogranuloma venereum (LGV) omp3 genes. We have previously sequenced omp2 from the LGV biovar and now describe the omp2 sequence for a trachoma biovariant. Amino acid sequence differences between biovariants were few but, significantly, these changes have altered the charge of both OMP2 and OMP3 such that the net charge of each protein differs between biovariants. These compensatory charge alterations have implications for the outer membrane organization of these proteins. In addition, examination of the OMP3 sequence suggests that OMP3 may be a lipoprotein.
Luminescences from localized states in InGaN epilayers (1997)

Optical spectra of the bulk three-dimensional InGaN alloys were measured using the commercially available light-emitting diode devices and their wafers. The emission from undoped InxGa1−xN(x&lt;0.1) was assigned to the recombination of excitons localized at the potential minima originating from the large compositional fluctuation. The emission from heavily impurity-doped InGaN was also pointed out related to the localized states.
The adverse effects of octreotide on wound healing in rats. (1997)

Octreotide acetate is a long-acting somatostatin analogue with protean physiologic effects. It is used primarily as an inhibitory paracrine hormone to treat a variety of medical and surgical disorders, including endocrine tumors and several gastrointestinal hypersecretory states. Because of octreotide's known inhibition of multiple trophic and anabolic hormones, we suspected that it may have deleterious effects on wound healing. Twenty-four rats were randomized to one of three groups: control, steroid (a negative control), or octreotide. Dorsal midline incisions were made and closed primarily. Wound-breaking strength measurements were performed 7 days later. The mean peak load (+/- standard error of the mean) for each group was calculated: control = 754 +/- 89 g; steroid = 378 +/- 32 g; and octreotide = 427 +/- 41 g. The difference between the control group and each of the other groups was statistically significant with P < 0.030. We conclude that octreotide has significant adverse effects on wound healing in the rat model and that these effects are comparable in magnitude to those caused by steroids.
Understanding the effects of changes on the cost‐effectiveness of regression testing techniques (2003)

Abstract Regression testing is an expensive testing process used to validate modified software. Regression test selection and test‐case prioritization can reduce the costs of regression testing by selecting a subset of test cases for execution, or scheduling test cases to meet testing objectives better. The cost‐effectiveness of these techniques can vary widely, however, and one cause of this variance is the type and magnitude of changes made in producing a new software version. Engineers unaware of the causes and effects of this variance can make poor choices in designing change integration processes, selecting inappropriate regression testing techniques, designing excessively expensive regression test suites and making unnecessarily costly changes. Engineers aware of causal factors can perform regression testing more cost‐effectively. This article reports the results of an embedded multiple case study investigating the modifications made in the evolution of four software systems and their impact on regression testing techniques. The results of this study expose tradeoffs and constraints that affect the success of techniques and provide guidelines for designing and managing regression testing processes. Copyright © 2003 John Wiley & Sons, Ltd.
Neurosteroid Hydroxylase CYP7B (2001)

The major adrenal steroid dehydroepiandrosterone (DHEA) enhances memory and immune function but has no known dedicated receptor; local metabolism may govern its activity. We described a cytochrome P450 expressed in brain and other tissues, CYP7B, that catalyzes the 7alpha-hydroxylation of oxysterols and 3beta-hydroxysteroids including DHEA. We report here that CYP7B mRNA and 7alpha-hydroxylation activity are widespread in rat tissues. However, steroids related to DHEA are reported to be modified at positions other than 7alpha, exemplified by prominent 6alpha-hydroxylation of 5alpha-androstane-3beta,17beta-diol (A/anediol) in some rodent tissues including brain. To determine whether CYP7B is responsible for these and other activities we disrupted the mouse Cyp7b gene by targeted insertion of an IRES-lacZ reporter cassette, placing reporter enzyme activity (beta-galactosidase) under Cyp7b promoter control. In heterozygous mouse brain, chromogenic detection of reporter activity was strikingly restricted to the dentate gyrus. Staining did not exactly reproduce the in situ hybridization expression pattern; post-transcriptional control is inferred. Lower level staining was detected in cerebellum, liver, and kidney, and which largely paralleled mRNA distribution. Liver and kidney expression was sexually dimorphic. Mice homozygous for the insertion are viable and superficially normal, but ex vivo metabolism of DHEA to 7alpha-hydroxy-DHEA was abolished in brain, spleen, thymus, heart, lung, prostate, uterus, and mammary gland; lower abundance metabolites were also eliminated. 7alpha-Hydroxylation of 25-hydroxycholesterol and related substrates was also abolished, as was presumed 6alpha-hydroxylation of A/anediol. These different enzyme activities therefore derive from the Cyp7b gene. CYP7B is thus a major extrahepatic steroid and oxysterol hydroxylase and provides the predominant route for local metabolism of DHEA and related molecules in brain and other tissues.
Impact of 1988 Drought on Agriculture (1988)

testifying to Congress in the early summer, called the drought and heat wave conclusive evidence that the predicted greenhouse effect was occurring, some scientists of a variety of backgrounds were saying privately that this year was only a precursor of things to come. The pattern of the drought as well as the several very hot years experienced in the 1980s seemed to them consistent with the predictions of the climate models that purport to take account of the effects of buildup of greenhouse gases.
A Kernel Density Window Clustering Algorithm for Radar Pulses (2008)

As radar signal environments become denser and more complex, the capability of high-speed and accurate signal analysis is required for ES (electronic warfare support) system to identify individual radar signals at real-time. In this paper, we propose the novel clustering algorithm of radar pulses to alleviate the load of signal analysis process and support reliable analysis. The proposed algorithm uses KDE (kernel density estimator) and its CDF (cumulative distribution function) to compose clusters considering the distribution characteristics of pulses. Simulation results show the good performance of the proposed clustering algorithm in clustering and classifying the emitters.
Strain estimation in phase-sensitive optical coherence elastography (2012)

We present a theoretical framework for strain estimation in optical coherence elastography (OCE), based on a statistical analysis of displacement measurements obtained from a mechanically loaded sample. We define strain sensitivity, signal-to-noise ratio and dynamic range, and derive estimates of strain using three methods: finite difference, ordinary least squares and weighted least squares, the latter implemented for the first time in OCE. We compare theoretical predictions with experimental results and demonstrate a ~12 dB improvement in strain sensitivity using weighted least squares compared to finite difference strain estimation and a ~4 dB improvement over ordinary least squares strain estimation. We present strain images (i.e., elastograms) of tissue-mimicking phantoms and excised porcine airway, demonstrating in each case clear contrast based on the sample's elasticity.