gebhart/patrepeval huggingface dataset:
Automated detection of point mutations using fluorescent sequence trace subtraction (1998)

The final step in the detection of mutations is to determine the sequence of the suspected mutant and to compare it with that of the wild-type, and for this fluorescence-based sequencing instruments are widely used. We describe some simple algorithms forcomparing sequence traces which, as part of our sequence assembly and analysis package, are proving useful for the discovery of mutations and which may also help to identify misplaced readings in sequence assembly projects. The mutations can be detected automatically by a new program called TRACE_DIFF and new types of trace display in our program GAP4 greatly simplify visual checking of the assigned changes. To assess the accuracy of the automatic mutation detection algorithm we analysed 214 sequence readings from hypermutating DNA comprising a total of 108 497 bases. After the readings were assembled there were 1232 base differences, including 392 Ns and 166 alignment characters. Visual inspection of the traces established that of the 1232 differences, 353 were real mutations while the rest were due to base calling errors. The TRACE_DIFF algorithm automatically identified all but 36, with 28 false positives. Further information about the software can be obtained from http://www.mrc-lmb.cam.ac.uk/pubseq/
Cycling to Reduce Air Pollution: The Environmental Protection Cycle Tour (1997)

Aetiology of pericardial calcifications can be multifactorial. Tuberculosis has been reported as the most common cause. Other known causes include uraemia, asbestosis, post-traumatic or postoperative. We report a rare case of pericardial calcification seen in a patient with established acute intermittent porphyria. A direct causal relationship cannot be established between porphyria and pericardial calcification, but it may be due to deposition of the porphyrin in the pericardium.
Regulation of cell growth by vitreous humour (1985)

Extracts of normal vitreous have been found to inhibit angiogenesis in two animal models: tumour-induced neovascularization in the rabbit corneal micropocket and retinal extract-induced angiogenesis in the chick chorioallantoic membrane assay. Using in vitro assays, we have found recently that an extract of bovine vitreous, free of hyaluronic acid, inhibits proliferation of cells in the aortic wall, i.e. endothelium and smooth muscle cells, as well as capillary and corneal endothelium. The inhibition is dose-dependent, as determined by either cell count or [3H]thymidine incorporation, and not due to cytotoxicity, as demonstrated with a double-label thymidine assay. The inhibitor is trypsin-sensitive and heat-stable (95 degrees C for 10 min). Conversely, proliferation of pericytes, lens epithelium and fibroblasts (dermal and corneal) was stimulated by the vitreous extract. This mitogenic activity was heat-labile. Growth of pigment epithelium and several tumour cell lines was unaffected. The data demonstrate that normal vitreous contains a heat-stable growth inhibitor specific for endothelium and smooth muscle cells, and a non-specific heat-labile mitogen. The paradoxical effect of this antiangiogenic factor on arterial and capillary contractile cells, smooth muscle and pericytes, suggests a basic difference in the regulation of the two vasculatures. The results suggest that a substance in normal vitreous may be important in controlling neovascularization that results from diabetic and other retinopathies, and could be useful for inhibiting tumour-induced angiogenesis.
Efficient White Organic Light‐Emitting Devices Based on Phosphorescent Platinum(II)/Fluorescent Dual‐Emitting Layers (2007)

Efficient white organic light-emitting devices with uncomplicated architectures are fabricated employing phosphorescent platinum(II) complexes containing extended π-conjugated cyclometalated ligands as a yellow-light source, and fluorescent material 9,10-bis-(β-naphthyl)-anthrene as a blue-light source. Peak external quantum (power) efficiencies of 11.8 % (18.4 lm W–1) are demonstrated (see figure).
Peroxisome biogenesis and peroxisome biogenesis disorders (2000)

Peroxisome assembly in mammals requires more than 15 genes. Two isoforms of the peroxisome targeting signal type 1 (PTS1) receptor, Pex5pS and Pex5pL, are identified in mammals. Pex5pS and Pex5pL bind PTS1 proteins. Pex5pL, but not Pex5pS, directly interacts with the PTS2 receptor, Pex7p, carrying its cargo PTS2 protein in the cytosol. Pex5p carrying the cargos, PTS1 and PTS2, docks with the initial site Pex14p in a putative import machinery, subsequently translocating to other components such as Pex13p, Pex2p, Pex10p and Pex12p, whereby the matrix proteins are imported. The peroxins, Pex3p, Pex16p and Pex19p, function in the assembly of peroxisomal membrane vesicles that precedes the import of matrix proteins. Hence, peroxisomes may form de novo and do not have to arise from pre-existing, morphologically recognizable peroxisomes. Impaired peroxisome assembly causes peroxisome biogenesis disorders such as Zellweger syndrome.
The clonal dependence of turion formation in the duckweed <i>Spirodela polyrhiza</i>—an ecogeographical approach (2013)

Formation of turions, the vegetative perennation organs, plays an important role in the survival strategy of Spirodela polyrhiza (L.) Schleiden. Turion formation [quantified as number of turions formed per frond; specific turion yield (SY)] was investigated in 27 clones collected from a wide geographical range. The Pearson correlation was tested with (1) duration of growing season (monthly average temperature of ≥10°C), (2) relative growth rate of the fronds, (3) longitude and latitude, and (4) several climatic parameters, in all possible single and multiple regressions. All single coefficients of determination were below 0.10. The highest correlation (R(2) = 0.61; adjusted for the number of explaining variables 0.54) was found in a multiple linear regression with the following five parameters: average temperatures over the year and during the growing season, duration of the growing season and precipitation over the year and during the growth period. All these parameters were shown to have significant contributions. This equation was used successfully to predict the SY of five newly isolated clones. Finally, on the basis of all 32 clones the following conclusions were drawn: The mean annual temperature has the highest impact. It is suggested that lower temperatures decrease the survival rate of turions and that adaptation refers to increasing SY. The different levels of SY in the clones (ranging from SY = 0.22 to 5.9) were detected even after several years of in vitro cultivation. It is therefore assumed that these adaptations to the climatic conditions are genetically determined.
Comparing Bayesian network classifiers (1999)

In this paper, we empirically evaluate algorithms for learning four Bayesian network (BN) classifiers: Naïve-Bayes, tree augmented Naïve-Bayes (TANs), BN augmented NaïveBayes (BANs) and general BNs (GBNs), where the GBNs and BANs are learned using two variants of a conditional independence based BN-learning algorithm. Experimental results show the GBNs and BANs learned using the proposing learning algorithms are competitive with (or superior to) the best classifiers based on both Bayesian networks and other formalisms, and that the computational time for learning and using these classifiers is relatively small. These results argue that BN classifiers deserve more attention in machine learning and data mining communities. 1 INTRODUCTION Classification is a fundamental task in fault diagnosis, pattern recognition and forecasting. In general, a classifier is a function that chooses a class label (from a group of predefined labels) for instances described by a set of features (attributes...
Solid-supported reagents in organic synthesis (1999)

The current interest in solid-phase organic synthesis has led to a renewed interest in a complementary technique in which solid supported reagents are used in solution phase chemistry. This technique obviates the need for attachment of the substrate to a solid-support, and enables the chemist to monitor the reactions using familiar analytical techniques. The purpose of this review is to increase awareness of the wide range of useful transformations which can be accomplished using solid-supported reagents.
Designing transcranial magnetic stimulation systems (2005)

We explain the process of designing optimized transcranial magnetic stimulation systems and outline a method for identifying optimal system parameters such as the number of turns, the capacitor size, the working voltage, and the size of the stimulation coil. The method combines field analysis, linear and nonlinear circuit analysis, and neural strength-duration response parameters. The method uses boundary-element analysis to predict the electric field as a function of depth, frequency, current, and excitation coil size. It then uses the field analysis to determine the inductance as a function of size and, in general, current when a saturable core is used. Circuit analysis allows these electric field computations to be indexed against system parameters, and optimized for total system energy and stimulation coil size. System optimizations depend on desired stimulation depth. A distinguishing feature of the method is that it inherently treats excitation frequency as an unknown to be determined from optimization.
Video content extraction and representation using a joint audio and video processing (1999)

Computer technology allows for large collections of digital archived material. At the same time, the increasing availability of potentially interesting data makes difficult the retrieval of desired information. Currently, access to such information is limited to textual queries or characteristics such as color or texture. The demand for new solutions allowing common users to easily access, store and retrieve relevant audio-visual information is becoming urgent. One possible solution to this problem is to hierarchically organize the audio-visual data so as to create a nested indexing structure which provides efficient access to relevant information at each level of the hierarchy. This work presents an automatic methodology to extract and hierarchically represent the semantics of the contents, based on a joint audio and visual analysis. Descriptions on each media (audio, video) are used to recognize higher level of meaningful structures, such as specific types of scenes, or, at the highest level, correlations beyond the temporal organization of information, allowing it to reflect classes of visual or audio or audio-visual types. Once a hierarchy is extracted from the data analysis, a nested indexing structure can be created to access relevant information at a specific level of detail, according to the user requirements.
A genomic region harboring the <i>Pl1</i> allele from the Peruvian cultivar JC072A confers purple cob on Japanese flint corn (<i>Zea mays</i> L.) (2018)

Purple corn is a maize variety (<i>Zea mays</i> L.) with high anthocyanin content. When purple corn is used as forage, its anthocyanins may mitigate oxidative stresses causing lower milk production in dairy cows. In this study, we analyzed quantitative trait loci (QTLs) for anthocyanin pigmentation of maize organs in an F<sub>2</sub> population derived from a cross between the Peruvian cultivar 'JC072A' (purple) and the inbred line 'Ki68' (yellowish) belonged to Japanese flint. We detected 17 significant QTLs on chromosomes 1-3, 6, and 10. Because the cob accounts for most of the fresh weight of the plant ear, we focused on a significant QTL for purple cob on chromosome 6. This QTL also conferred pigmentation of anther, spikelet, leaf sheath, culm, and bract leaf, and was confirmed by using two F<sub>3</sub> populations. The gene <i>Pl1</i> (<i>purple plant 1</i>) is the most likely candidate gene in this QTL region because the amino acid sequence encoded by <i>Pl1-JC072A</i> is similar to that of an Andean allele, <i>Pl-bol3</i>, which is responsible for anthocyanin production. The markers designed for the <i>Pl1</i> alleles will be useful for the breeding of F<sub>1</sub> lines with anthocyanin pigmentation in cobs.
Selective Inhibitors of Bacterial Phosphopantothenoylcysteine Synthetase (2009)

Bacterial phosphopantothenolycysteine synthetase (PPCS) catalyzes the formation of phosphopantothenoylcysteine (PPC) from (R)-phosphopantothenate, l-cysteine, and cytidine-5'-triphosphate (CTP) and has been shown to be essential for growth and survival. The reaction proceeds through a phosphopantothenoyl cytidylate, mixed anhydride intermediate. Both structural and kinetic characterization studies on PPCS have shown differences in the nucleobase binding site between the bacterial and human enzyme. We report for the first time the design and synthesis of mimics of the phosphopantothenoyl cytidylate, which proved to be potent inhibitors of PPCS. These compounds were evaluated in vitro against PPCS from human and several species of bacteria and showed marked selectivity (up to 1000-fold) toward the bacterial enzymes. A phosphodiester intermediate mimic was the most potent of the compounds synthesized and displayed slow-onset, tight-binding kinetics toward E. faecalis PPCS.
Thermochemical Biomass Gasification: A Review of the Current Status of the Technology (2009)

A review was conducted on the use of thermochemical biomass gasification for producing biofuels, biopower and chemicals. The upstream processes for gasification are similar to other biomass processing methods. However, challenges remain in the gasification and downstream processing for viable commercial applications. The challenges with gasification are to understand the effects of operating conditions on gasification reactions for reliably predicting and optimizing the product compositions, and for obtaining maximal efficiencies. Product gases can be converted to biofuels and chemicals such as Fischer-Tropsch fuels, green gasoline, hydrogen, dimethyl ether, ethanol, methanol, and higher alcohols. Processes and challenges for these conversions are also summarized.
The Cell Wall of Prototheca zopfii (1968)

SUMMARY Cell walls of Prototheca zopfii kruger 236/65 were prepared by differential centrifugation after disruption of the organisms in a French press. The isolated walls were free from whole organisms and subcellular particles as shown by examination by light and electron microscopy. A quantitative analysis of the walls was made with respect to total nitrogen, phosphorus, ash and lipid. Paper chromatography of hydrolysates of walls showed glucose, mannose, glucosamine and twelve amino acids. A quantitative amino acid analysis was made by ion-exchange chromatography; trace amounts of several other amino acids were detected. The structure of the walls was studied before and after treatment with NaOH and a variety of hydrolytic enzymes. The results are compared with those obtained by other workers with various species of Chlorella, Aspergillus and yeasts. The results are discussed with reference to the taxonomic position of Prototheca zopfii.
Stepping up to the computer (2010)

I disagree with John Fang’s oversimplified statement about the internet. Any technology is just a tool. Its value depends on how people use it. Nuclear power, for example, can provide heat and light for our homes and businesses, or it can be developed as a deadly weapon. For scientists nowadays, the internet is essential for research. It saves us from having to run to the library to make a photocopy of that paper we need; instead, we can download the electronic file at our desks with a few clicks.I believe Fang’s observation stems from young people’s frequent misuse of the internet. In my opinion, well-designed homework is the key to getting students to find answers in nature rather than from computers. Teachers who regularly assign homework whose answers are easily found on the internet perhaps need to examine their teaching methods.When I taught Newton’s third law of motion, I demonstrated how to use a balloon to propel a small cart and explained why it worked. Then I gave students the homework assignment of finding other ways to move the cart or to improve its efficiency, and I required that they make their own carts. They could search the internet for instructions, but they eventually had to make a real cart, which involved their using technical skills. Since grading of the homework was based on how far the cart could go and how innovative the method was to propel the cart, my students spent much more time on testing their carts than in front of the computers. As a teacher, I also had to spend a lot of time on the internet so that I could judge whether the students’ designs were really their own.Finally, let me underscore that the proper uses of science and technology are keys to making life better, for ourselves and for the planet.© 2010 American Institute of Physics.
Object-oriented modeling of patients in a medical federation (2001)

This research explores the development of an object-oriented model to support inter-operation of simulations within a federation for the purpose of conducting medical analysis and training over a distributed infrastructure. The medical federation is referred to as the combat trauma patient simulation system and is composed using high level architecture. The infrastructure contains components that were separately developed and are heterogeneous in nature. This includes a general anatomical computer database capable of generating human injuries, referred to as operational requirements-based casualty assessment, an animated mannequin called the human patient simulator, and other components. The research develops an object model that enables bodily injury data to be shared across the simulation, conducts analysis on that data, and considers possible applications of the technique in expanded medical infrastructures.
A simulation study of turbofan engine deterioration estimation using Kalman filtering techniques (1991)

Deterioration of engine components may cause off-normal engine operation. The result is an unecessary loss of performance, because the fixed schedules are designed to accommodate a wide range of engine health. These fixed control schedules may not be optimal for a deteriorated engine. This problem may be solved by including a measure of deterioration in determining the control variables. These engine deterioration parameters usually cannot be measured directly but can be estimated. A Kalman filter design is presented for estimating two performance parameters that account for engine deterioration: high and low pressure turbine delta efficiencies. The delta efficiency parameters model variations of the high and low pressure turbine efficiencies from nominal values. The filter has a design condition of Mach 0.90, 30,000 ft altitude, and 47 deg power level angle (PLA). It was evaluated using a nonlinear simulation of the F100 engine model derivative (EMD) engine, at the design Mach number and altitude over a PLA range of 43 to 55 deg. It was found that known high pressure turbine delta efficiencies of -2.5 percent and low pressure turbine delta efficiencies of -1.0 percent can be estimated with an accuracy of + or - 0.25 percent efficiency with a Kalman filter. If both the high and low pressure turbine are deteriorated, the delta efficiencies of -2.5 percent to both turbines can be estimated with the same accuracy.
Digital Subscriber Line Terminals for Use with Correlated Line Codes (1987)

This paper is a mathematical analysis of digital subscriber lines that use adaptive decision feedback equalization (DFE). Adaptive transversal feedforward filters (FFF) and feedback filters (FBF) with baud rate sampling are assumed. In order that all block codes are considered in the model, correlation between the values of the transmitted symbol values is included. Additionally, added noise is not assumed to be white, to permit the eyaluation of the effects of near end crosstalk and residual echo noise. It is shown that the correlation between the transmitted symbols causes the FBF to adapt differently than they usually do (i.e., cancel intersymbol interference within the range of the FBF) in two ways: the FBF uses the correlation between transmitted symbols to reduce the intersymbol interference outside of its range, and a bias vector is added to the FBF tap weights that adjusts future slicing levels to account for the variable likelihood of future transmitted symbol values. It is found that the received signal-to-noise ratio is approximately a linear function of loop insertion loss when the loss is high and noise is low.
Growth and spectral properties of Pr<sup>3+</sup>-doped Y<sup>3</sup>Al<sup>5</sup>O<sup>12</sup> crystal for potential use in all-solidstate visible laser (2016)

Pr3+-doped Y3Al5O12 (Pr:YAG) single crystal has been grown by the Czochralski technique. The room temperature absorption spectrum, emission spectrum, and fluorescence decay curves of Pr:YAG single crystal were studied systematically. Strong absorption peaks in the blue region corresponding to 3H4→3P2,1,0 + 1I6 transitions and emission peaks in the visible region originating from the 3P1, 3P0 and 1D2 levels of Pr3+ are observed. The emission cross-sections of four main promising laser transitions at 488, 566, 611 and 638 nm were estimated separately. Results show that Pr:YAG single crystal is an excellent candidate for all-solid-state visible laser material that can be pumped by blue laser diode.
Runtime visualisation of object oriented software (2003)

Software is inherently dynamic, yet much of the analysis and comprehension processes focus entirely on the static source code of the software. This paper looks at how software visualisation offers a way to aid comprehension by displaying both static and dynamic aspects of a piece of software. A new visualisation is presented with specific focus on a class level summary view.
The activation mechanism of class‐C G‐protein coupled receptors (2004)

Summry— Class‐C G‐protein coupled receptors (GPCRs) represent a distant group among the large family of GPCRs. This class includes the receptors for the main neurotransmitters, glutamate and γ‐aminobutyric acid (GABA), and the receptors for Ca 2+ , some taste and pheromone molecules, as well as some orphan receptors. Like any other GPCRs, class‐C receptors possess a heptahelical domain (HD) involved in heterotrimeric G‐protein activation, but most of them also have a large extracellular domain (ECD) responsible for agonist recognition and binding. In addition, it is now well accepted that these receptors are dimers, either homo or heterodimers. This complex architecture raises a number of important questions. Here we will discuss our view of how agonist binding within the large ECD triggers the necessary change of conformation, or stabilize a specific conformation, of the heptahelical domain leading to G‐protein activation. How ligands acting within the heptahelical domain can change the properties of these complex macromolecules.
The Interaction of Plasticizers and Polymers (1945)

Abstract The general problem of plasticizer compatibility is discussed, and it is suggested that a comparative measure of compatibility can be obtained from experiments which measure polymer-plasticizer interactions ( w ). Experiments are described which measure the viscosity of dilute polymer solutions in suitable mixed solvents containing the plasticizer in question. The slope of the η sp /c−c curve is shown to be related to the equilibrium extent of swelling of the polymer in the pure plasticizer and, in general, the slope of the curve is a good comparative measure of the plasticizer's compatibility. The effects of temperature and composition of the mixed solvent are also discussed. The experiments are considered in the light of a previous theory of the effect of solvent on the η sp /c ratio: the results do not support the suggested view that the slope of the η sp /c−c curve is a simple linear function of w/kT .