gebhart/patrepeval huggingface dataset:
Functional expression in yeast and characterization of a clofibrate-inducible plant cytochrome P-450 (CYP94A1) involved in cutin monomers synthesis (1998)

The chemical tagging of a cytochrome P-450-dependent lauric acid omega-hydroxylase from clofibrate-treated Vicia sativa seedlings with [1-14C]11-dodecynoic acid allowed the isolation of a full-length cDNA designated CYP94A1. We describe here the functional expression of this novel P-450 in two Saccharomyces cerevisiae strains overproducing their own NADPH-cytochrome P-450 reductase or a reductase from Arabidopsis thaliana. The results show a much higher efficiency of the yeast strain overproducing the plant reductase compared with the yeast strain overproducing its own reductase for expressing CYP94A1. The methyl end of saturated (from C-10 to C-16) and unsaturated (C18:1, C18:2 and C18:3) fatty acids was mainly oxidized by CYP94A1. Both E/Z and Z/E configurations of 9, 12-octadecadienoic acids were omega-hydroxylated. Lauric, myristic and linolenic acids were oxidized with the highest turnover rate (24 min-1). The strong regioselectivity of CYP94A1 was clearly shifted with sulphur-containing substrates, since both 9- and 11-thia laurate analogues were sulphoxidized. Similar to animal omega-hydroxylases, this plant enzyme was strongly induced by clofibrate treatment. Rapid CYP94A1 transcript accumulation was detected less than 20 min after exposure of seedlings to the hypolipidaemic drug. The involvement of CYP94A1 in the synthesis of cutin monomers and fatty acid detoxification is discussed.
A Multi-Criteria Decision Making Method Based on Fuzzy Outranking Relation (1990)

In selecting the best project in multi-criteria decision making problems, the imperfect information of consequence and the vague preference of the decision maker(DM) would make the decision analysis more complex together with the conflict of several criteria. In this context, a method is proposed to deal the fuzzy information mentioned before instead of reducing it to a single representative value. And, based on the given imprecise information, projects are ranked completely or partially according to DM's vague preference. The procedure consists, for each pair of projects, of calculating the degree of supporting over all criteria and the degree of opposing with respect to each criterion for their outranking relation. Together with weights for each criterion, these indices produce fuzzy outranking relations for each pair of projects. And a complete or partial ranking of projects is obtained according to outranking degrees considering the interdependence among projects.
When and how to develop domain-specific languages (2005)

Domain-specific languages (DSLs) are languages tailored to a specific application domain. They offer substantial gains in expressiveness and ease of use compared with general-purpose programming languages in their domain of application. DSL development is hard, requiring both domain knowledge and language development expertise. Few people have both. Not surprisingly, the decision to develop a DSL is often postponed indefinitely, if considered at all, and most DSLs never get beyond the application library stage.Although many articles have been written on the development of particular DSLs, there is very limited literature on DSL development methodologies and many questions remain regarding when and how to develop a DSL. To aid the DSL developer, we identify patterns in the decision, analysis, design, and implementation phases of DSL development. Our patterns improve and extend earlier work on DSL design patterns. We also discuss domain analysis tools and language development systems that may help to speed up DSL development. Finally, we present a number of open problems.
Inferring the Rate and Time-Scale of Dengue Virus Evolution (2003)

Dengue is often referred to as an emerging disease because of the rapid increases in incidence and prevalence that have been observed in recent decades. To understand the rate at which genetic diversification occurs in dengue virus and to infer the time-scale of its evolution, we employed a maximum likelihood method that uses information about times of virus sampling to estimate the rate of molecular evolution in a large number of viral envelope (E) gene sequences and to place bounds around the dates of appearance of all serotypes and specific genotypes. Our analysis reveals that dengue virus generally evolves according to a molecular clock, although some serotype-specific and genotype-specific rate differences were observed, and that its origin is more recent than previously suggested, with the virus appearing approximately 1,000 years ago. Furthermore, we estimate that the zoonotic transfer of dengue from sylvatic (monkey) to sustained human transmission occurred between 125 and 320 years ago, that the current global genetic diversity in the four serotypes of dengue virus only appeared during the past century, and that the recent rise in genetic diversity can be loosely correlated both to human activities such as population growth, urbanization, and mass transport and to the emergence of dengue hemorrhagic fever as a major disease problem.
Characterizing smiles in the context of video phone data compression (1996)

We propose an approach to characterizing human smiles based on the principal component analysis of the facial motion parameters. Motion vectors of a set of feature points are derived from neutral and smiling face images and a feature space is built based on those motion vectors. The principal component analysis technique is used for dimension reduction and some preliminary results of smile characterization are obtained.
The Synthesis of 6-Aminomethyl-5,6,7,8-Tetrahydropterin (1988)

6-Aminomethyl-5,6,7,8-tetrahydropterin has been prepared by reduction of 2-acetamido-6-cyanopteridin-4(3H)-one* to 2-acetamido-6-aminomethyl- 5,6,7,8-tetrahydropteridin-4(3H)-one followed by acid hydrolysis. The hitherto undescribed 6-cyanopterin was prepared by careful hydrolysis of the 2-acetamido compound prepared by dehydration of the oxime derived from 2-acetamido-6-formylpteridin-4(3H)-one. The latter was prepared by selenium dioxide oxidation of the methyl compound. Oxidation of 6-aminomethyl-5,6,7,8-tetrahydropterin at neutral pH appears to proceed with significant side-chain loss in Tris buffer but not in phosphate buffer.
Differential Effects of Estrogen and Progesterone on AT<sub>1</sub>Receptor Gene Expression in Vascular Smooth Muscle Cells (2000)

Because AT(1) receptor regulation plays a pivotal role in the pathogenesis of hypertension and atherosclerosis, the differential effects of estrogen and progesterone on the expression of this gene may in part explain the potentially counteracting effects of these reproductive hormones on the incidence of postmenopausal cardiovascular diseases.
The lightweight and large porous mesh concept for hernia repair (2005)

In modern hernia surgery, there are two competing mesh concepts which often lead to controversial discussions, on the one hand the heavyweight small porous model and on the other, the lightweight large porous hypothesis. The present review illustrates the rationale of both mesh concepts and compares experimental data with the first clinical data available. In summary, the lightweight large porous mesh philosophy takes into consideration all of the recent data regarding physiology and mechanics of the abdominal wall and inguinal region. Furthermore, the new mesh concept reveals an optimized foreign body reaction based on reduced amounts of mesh material and, in particular, a significantly decreased surface area in contact with the recipient host tissues by the large porous model. Finally, recent data demonstrate that alterations in the extracellular matrix of hernia patients play a crucial role in the development of hernia recurrence. In particular, long-term recurrences months or years after surgery and implantation of mesh can be explained by the extracellular matrix hypothesis. However, if the altered extracellular matrix proves to be the weak area, the decisive question is whether the amount of material as well as mechanical and tensile strength of the surgical mesh are really of significant importance for the development of recurrent hernia. All experimental evidence and first clinical data indicate the superiority of the lightweight large porous mesh concept with regard to a reduced number of long-term complications and particularly, increased comfort and quality of life after hernia repair.
RBP2 is an MRG15 complex component and down‐regulates intragenic histone H3 lysine 4 methylation (2007)

MRG15 is a conserved chromodomain protein that associates with histone deacetylases (HDACs) and Tip60-containing histone acetyltransferase (HAT) complexes. Here we further characterize MRG15-containing complexes and show a functional link between MRG15 and histone H3K4 demethylase activity in mammalian cells. MRG15 was predominantly localized to discrete nuclear subdomains enriched for Ser(2)-phosphorylated RNA polymerase II, suggesting it is involved specifically with active transcription. Protein analysis of the MRG15-containing complexes led to the identification of RBP2, a JmjC domain-containing protein. Remarkably, over-expression of RBP2 greatly reduced the H3K4 methylation in culture human cells in vivo, and recombinant RBP2 efficiently removed H3K4 methylation of histone tails in vitro. Knockdown of RBP2 resulted in increased H3K4 methylation levels within transcribed regions of active genes. Our findings demonstrate that RBP2 associated with MRG15 complex to maintain reduced H3K4 methylation at transcribed regions, which may ensure the transcriptional elongation state.
Local Function Approximation in Evolutionary Algorithms for the Optimization of Costly Functions (2004)

We develop an approach for the optimization of continuous costly functions that uses a space-filling experimental design and local function approximation to reduce the number of function evaluations in an evolutionary algorithm. Our approach is to estimate the objective function value of an offspring by fitting a function approximation model over the k nearest previously evaluated points, where k=(d+1)(d+2)/2 and d is the dimension of the problem. The estimated function values are used to screen offspring to identify the most promising ones for function evaluation. To fit function approximation models, a symmetric Latin hypercube design (SLHD) is used to determine initial points for function evaluation. We compared the performance of an evolution strategy (ES) with local quadratic approximation, an ES with local cubic radial basis function (RBF) interpolation, an ES whose initial parent population comes from an SLHD, and a conventional ES. These algorithms were applied to a twelve-dimensional (12-D) groundwater bioremediation problem involving a complex nonlinear finite-element simulation model. The performances of these algorithms were also compared on the Dixon-Szego test functions and on the ten-dimensional (10-D) Rastrigin and Ackley test functions. All comparisons involve analysis of variance (ANOVA) and the computation of simultaneous confidence intervals. The results indicate that ES algorithms with local approximation were significantly better than conventional ES algorithms and ES algorithms initialized by SLHDs on all Dixon-Szego test functions except for Goldstein-Price. However, for the more difficult 10-D and 12-D functions, only the cubic RBF approach was successful in improving the performance of an ES. Moreover, the results also suggest that the cubic RBF approach is superior to the quadratic approximation approach on all test functions and the difference in performance is statistically significant for all test functions with dimension d/spl ges/4.
EF-1[alpha] Is Associated with a Cytoskeletal Network Surrounding Protein Bodies in Maize Endosperm Cells. (1996)

By using indirect immunofluorescence and confocal microscopy, we documented changes in the distribution of elongation factor-1[alpha] (EF-1[alpha]), actin, and microtubules during the development of maize endosperm cells. In older interphase cells actively forming starch grains and protein bodies, the protein bodies are enmeshed in EF-1[alpha] and actin and are found juxtaposed with a multidirectional array of microtubules. Actin and EF-1[alpha] appear to exist in a complex, because we observed that the two are colocalized, and treatment with cytochalasin D resulted in the redistribution of EF-1[alpa]. These data suggest that EF-1[alpha] and actin are associated in maize endosperm cells and may help to explain the basis of the correlation we found between the concentration of EF-1[alpha] and lysine content. The data also support the hypothesis that the cytoskeleton plays a role in storage protein deposition. The distributions of EF-1[alpha] actin, and microtubules change during development. We observed that in young cells before the accumulation of starch and storage protein, EF-1[alpha], actin, and microtubules are found mainly in the cell cortex or in association with nuclei.
NER systems that suit user's preferences (2006)

We describe a method based on "tweaking" an existing learned sequential classifier to change the recall-precision tradeoff, guided by a user-provided performance criterion. This method is evaluated on the task of recognizing personal names in email and newswire text, and proves to be both simple and effective.
A Novel Frequency Control Loop for Tunable Notch Filters (2011)

In this paper, a novel frequency control loop system for tunable notch filters is presented. The frequency control loop is designed for automatically tuning a microelectromechancial systems tunable notch filter, which has 22-dB rejection in the notch band and less than 0.8-dB insertion loss over a 5-MHz passband bandwidth in the International Mobile Telecommunications band (2.1 GHz). The filter frequency control loop is based on sensing the reflection phase change of a reference signal (in this case, the transmitter carrier) and is developed to track the transmitter operation frequency.
Quasi-cyclic LDPC codes based on D and Q matrices through progressive edge growth (2007)

We propose a general method for constructing regular and irregular quasi-cyclic LDPC codes based on the modified PEG (progressive edge growth) graph. The idea of permutation vector is introduced. Through permutation vectors, the QC-LDPC codes based on arbitrary circulant permutation matrices, which are not limited to identity matrix, Q-matrix or D-matrix, can be generated with flexible parameters such as block length, code rate, degree distribution. Simulation results demonstrate that QC-LDPC codes using the new PEG algorithm show an error correction performance comparable to the random LDPC codes based on the traditional PEG algorithm. In addition, the PEG QC-LDPC codes have more hardware-friendly parity check matrices than the random PEG LDPC codes and can fulfill linear-time encoding. The QC-LDPC codes based on D-matrix and Q-matrix are more suitable to be used in QC-LDPC codes than identity matrix because they outperform that of identity matrix by 0.1-0.2 dB in the new PEG algorithm.
Pumping liquids using asymmetric electrode arrays (2000)

Following a general symmetry argument, I suggest using locally asymmetric electric geometries to pump liquid in channels or drive droplets on surfaces. This strategy, which requires no global gradient in the pumping direction, should be of interest for microfluidic devices and micro-electro-mechanical systems. A practical realization consists in using polar periodic arrays of electrodes addressed by an ac voltage difference. A simple electro-osmotic model provides an estimate of the pumping velocities achievable.
Isolation and Characterization of Antigen-Specific Plasmablasts Using a Novel Flow Cytometry–Based Ig Capture Assay (2017)

We report the development of a novel flow cytometry-based Ig capture assay (ICA) for the identification and sorting of individual Ab-secreting cells based on their Ag reactivity. The ICA represents a fast and versatile tool for single-cell sorting of peripheral plasmablasts, streamlining subsequent Ab analysis, and cloning. We demonstrate the utility of the assay by isolating Ag-reactive plasmablasts from cryopreserved PBMC obtained from volunteers vaccinated with a recombinant HIV envelope protein. To show the specificity of the ICA, we produced Ag-specific Abs from these cells and subsequently verified their Ag reactivity via ELISA. Furthermore, we used the ICA to track Ag-specific plasmablast responses in HIV-vaccine recipients over a period of 42 d and performed a head-to-head comparison with a conventional B cell ELISpot. Results were highly comparable, highlighting that this assay is a viable alternative for monitoring Ag-specific plasmablast responses at early time points after infection or vaccination. The ICA provides important added benefits in that phenotypic information can be obtained from the identified Ag-specific cells that can then be captured for downstream applications such as B cell sequencing and/or Ab cloning. We envisage the ICA as being a useful tool in Ab repertoire analysis for future clinical trials.
Sequential Rank Tests II. Modified Two-Sample Procedures (1966)

This paper describes modifications of the sequential, two-sample, grouped, rank tests developed earlier. A modified, sequential, configural rank test is discussed in some detail and is a procedure based on rerankings of observations as new groups of observations are obtained sequentially. A numerical application is given. Monte Carlo results are presented on the modified, sequential, configural rank test and compared with earlier studies. Proofs of termination of the test are reported and outstanding unsolved problems noted.
Nanoparticle decorated fibrous silica membranes exhibiting biomimetic superhydrophobicity and highly flexible properties (2011)

Inspired by the self-cleaning lotus leaf, here we report the fabrication of flexible fluorinated silica nanofibrous membranes with biomimetic non-wettable surfaces by electrospinning blend solutions of poly(vinyl alcohol) (PVA) and silica gel in the presence of silica nanoparticles, followed by calcination and fluoroalkylsilane (FAS) modification. The resultant silica nanofibers exhibited a lotus-leaf-like structure with numerous nanoparticles decorated on the fiber surfaces due to the rapid phase separation in electrospinning and calcination processing. The content of silica nanoparticles incorporated into the fibers proved to be the key factor affecting the fiber surface morphology and wettability. The fluorinated silica fibrous membranes containing 38.8 wt% silica nanoparticle showed the highest water contact angle (WCA) of 155°, oil contact angle (OCA) of 143°, orange juice contact angle (OJCA) of 142°, and milk contact angle (MCA) of 137°. Additionally, the fluorinated silica membranes exhibited good flexibility and the flexibility was also characterized by KES-FB2S. We believe that this new class of inorganic membranes is particularly promising for the development of high-temperature filtration, novel easy-clean coatings, and even flexible electronics.
Low‐Temperature ABC‐Type Atomic Layer Deposition: Synthesis of Highly Uniform Ultrafine Supported Metal Nanoparticles (2010)

Sheltered growth: A novel atomic layer deposition (ALD) method to synthesize highly uniform ultrafine supported metal nanoparticles is described. The ALD process includes growing protected metal nanoparticles and new support layers simultaneously at low temperature. In the final stage, the activation of the metal nanoparticles can be achieved by removing the protective ligands through calcination or reduction at elevated temperature (see picture). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A neural network approach towards reinforcing smart home security (2010)

In today's context, it is common to leave the house unattended as people are busy catching up with their tight daily schedule. Therefore, most people have chosen the home security system as the most reliable way to protect their home. However, the existing security mechanism provided by smart home is lack of intelligence for higher level decision making and action taking. Furthermore, the current security management of smart home is usually predefined by user. Thus, for consequences that are out of the defined scopes, chances to trigger false alarm are very high. Besides, the environment of each smart home is difference and the culture is also different from country to country, so the predefined security instructions may not work well or they may not suitable for all scenarios. Therefore, an intelligent algorithm with self learning ability must be adopted for smart home system in order to take adequate actions against the evaluated environment and decide for the necessary actions. Neural networks have been proposed in this paper where they are adaptive statistical models based on an analogy with the structure of the brain. The intelligence of the smart home should be able to analyze the information gathered by the sensors and detectors and to respond based on the analysis and the experiences gained via the neural networks. Neural network is chosen because they have the learning ability to estimate the parameters of some populations using a small number of examples at a time. When come to neural network learning process, there are several learning algorithms that could be applied, which can learn through pattern recognition, movement recognition, action recognition and so forth.
Activation of the guinea pig alternative complement pathway by mouse IgA immune complexes. (1982)

Activation of the complement system by IgA was investigated with immune complexes containing a mouse IgA myeloma protein with specificity for phosphorylcholine linked to bovine serum albumin (PC-BSA). These IgA anti-PC-BSA immune complexes activated the alternative complement pathway in mouse and guinea pig serum, while human complement was not affected. The activation proceeded with consumption of C3 but little or no consumption of C5. C3 did not bind to the IgA immune complexes during complement activation although it did bind covalently to IgG immune complexes. It is suggested that IgA immune complexes do not supply a suitable surface for C3 binding and effective alternative pathway convertase assembly; therefore, cleavage is limited and occurs primarily in the fluid phase. Without C3 binding, C5 cleavage does not occur nor can the alternative pathway activation proceed to the amplification step.
Diaphragmatic and genioglossal electromyogram responses to CO2 rebreathing in humans (1981)

To assess the relationship between central control of upper airway and respiratory muscle, simultaneously recorded diaphragmatic electromyogram (EMGdi) and genioglossal EMG (EMG ge) responses to CO2 rebreathing were compared in five supine volunteers. Both EMGs were quantitated in terms of inspiratory peak moving time-average activity. In all subjects both EMGdi and EMGge increased linearly with increasing alveolar CO2 pressure (r = 0.93 +/- 0.04 and 0.87 +/- 0.07, respectively), resulting in a significantly linear EMGge vs. EMGdi relationship (r = 0.91 +/- 0.04). CO2 response slopes of both EMGs were similar and linearly related (r = 0.96, P less than 0.001) such that subjects with low EMGdi response also had a low EMGge response and vice versa. Although the onset of EMGge activity preceded that of EMGdi, and the pattern of both EMGs were different, inspiration duration of both EMGs were similar. These data indicate that in humans both diaphragm and genioglossus muscle share similar control mechanisms and suggest that upper airway function is intimately related to the regulation of breathing.