gebhart/patrepeval huggingface dataset:
Microbial and mineralogical analysis of aluminum-rich precipitates that occlude porosity in a failed anoxic limestone drain, Monongalia County, West Virginia (1996)

Anoxic limestone drains (ALD) are among the many technologies being tested to reduce acidity and remove metals from streams affected by acid mine drainage (AMD). Built at the outflows of acidic drainage, these trenches are filled with limestone to add alkalinity. The trenches are covered to keep them anoxic so that iron remains in solution and does not coat the limestone gravel. Many ALD`s fail within months of construction as the limestone gravel porosity is reduced because of cementation by aluminum-rich substances. The Ridenour Rural and Abandoned Mineland Program (RAMP) experimental ALD site near Morgantown, WV, was built in 1992 to treat drainage that flows into the Monongahela River from old adits and seeps associated with a deep mine in the Pittsburgh Coal bed. Three drains were built to collect different seeps. Design of the drains included burying ASTM C-33 No. 57 gradation limestone gravel ({approximately}1 in.) in pits that were lined with plastic and then covered with soil. A stand pipe at the outlet end of the drains raises the water level to that mine water percolates through continuously submerged limestone. During construction of the drains, monitoring wells were installed, and galvanized wire mesh cages filled with limestone gravelmore » were suspended downhole at the end of fishing line in order to monitor progressive changes in the limestone gravel surfaces. Within six months, two of the three drains were experiencing severely reduced flow. A series of downhole experiments were designed at the Ridenour site to learn why porosity was lost. The experiment focused on the drain composed of 108 metric tons of limestone, the White Drain, that had gravel coated with a white precipitate.« less
Beyond Industrialization: The Prescription Food System (1998)

Food Consumption/Nutrition/Food Safety, Industrial Organization
HPLC analyses of cultures of <i>Phoma</i> spp.: Differentiation among groups and species through secondary metabolite profiles (2000)

The metabolite profiles of 26 isolates of the blackleg fungus (Leptosphaeria maculans (Desm.) Ces. et de Not., asexual stage Phoma lingam (Tode ex Fr.) Desm.), obtained from diverse parts of the world (part of the International Blackleg Crucifer Network collection), were studied utilizing specific culture conditions, HPLC analysis, and a set of chemical markers. This fungus is the causative agent of blackleg disease of brassica oilseeds; a virulent strain of the pathogen has caused significant rapeseed (Brassica napus L., and B. rapa L.) and canola (B. napus L., and B. rapa L.) losses in Canada, and is also considered a serious agricultural problem worldwide. Effective surveys of blackleg epidemics require simple and reliable analytical methodology to differentiate among the diverse groups of isolates. The chemical analysis of phytotoxins and related secondary metabolites is perhaps one of the most discriminating and the least ambiguous methods for differentiation of Phoma blackleg isolates. Following HPLC analyses, the 26 isolates could be placed in three main groups, irrespective of country of origin: isolates producing phomamide and sirodesmins, isolates producing indolyl dioxopiperazines, and isolates producing polyketides. Discussion of the implications of our findings and suggestions for species reclassification are provided.
Adsorption of Fibrinogen on Thin Oriented Poly(Tetrafluoroethylene) (PTFE) Fibres Studied by Scanning Force Microscopy (1994)

We have investigated fibrinogen adsorption on ordered poly(tetrafluoroethylene), PTFE, fibres deposited on hydrophilic and hydrophobic silicon substrates. Fibrinogen molecules appear to adsorb with their long axis perpendicular to the fibre direction for PTFE fibres having widths of less than 100 nm. On these thin fibres, fibrinogen apparently forms close packed bands or clusters, consisting of small integer numbers of molecules arranged parallel to each other. On broader (> 100 nm) PTFE fibres, the fibrinogen forms two dimensional networks. The orientation of the molecules in these networks is random in the central flat part of the fibres but perpendicular to the fibre direction at the fibre edges. As a tentative explanation, we propose that the observed orientation may be linked to the radius of curvature of the fibre surface.
A gibberellin responsive wheat gene has homology to yeast carboxypeptidase Y. (1987)

An earlier report (Baulcombe, D. C., and Buffard, D. (1983) Planta 157, 493-501) described the isolation of cDNA clones from mRNAs which are produced in increased amounts when aleurone layers of wheat are treated with gibberellic acid. It is shown here that for one of those cDNAs (2473) the change in level of mRNA in aleurone parallels the change in level of alpha-amylase mRNA. This result was obtained in experiments where the level of gibberellic acid was varied and also when the mRNA was isolated from wheat genotypes which varied in ability to respond to gibberellic acid. In contrast to this, the pattern of 2437 mRNA accumulation in immature grains and in leaf tissue was quite distinct from the pattern of alpha-amylase mRNA accumulation. Analysis of wheat DNA showed that the 2437 mRNA is encoded by a small family of genes located on the short arm of the group 6 chromosomes. One member of this gene family was cloned and sequenced. The coding sequence is interrupted by eight introns and encodes a protein of Mr 55,433. By using hybridization probes from the 5' exon in an S1 nuclease protection assay it was shown that the 2437 mRNA was produced in aleurones (coordinately with alpha-amylase) and in immature grains (not coordinately with alpha-amylase). However, sequence comparison of 1 kilobase of the 5'-flanking region with the sequence of alpha-amylase genes provided no indication of the regulatory elements which would be active in aleurone cells. The protein sequence deduced from the gene sequence has extensive homology with the yeast carboxypeptidase Y, especially in the active site and substrate binding regions. This homology is greater than with the carboxypeptidase I from barley. It is suggested therefore that there are several types of carboxypeptidase encoded in the cereal genome. The sequence of the 2437 protein would represent one of these types and the barley carboxypeptidase I, another.
Interferometric Testing Of Aspheric Surfaces (1987)

Methods for testing aspheric surfaces fall into two categories: null tests and non-null tests. In a null test, accessory optics are included in the test setup to cancel the asphericity of the aspheric optics under test. Thus, if the aspheric optics under test are perfect, an interferometric test will give straight equally-spaced fringes. In a non-null test, non-straight, non-equally-spaced fringes will be obtained even if the optics under test are perfect. As long as computer analysis is available and the fringe spacing is sufficiently large that the fringes can be detected, non-null tests are as good as null tests, and they are generally easier to perform. Non-null tests can measure the wavefront directly, or a shearing interferometer test can be performed which measures the slope of the wavefront, rather than the wavefront itself. A shearing interferometer test has the advantage that for a given wavefront aberration, fewer interference fringes are obtained; however it has the disadvantage that the measurement accuracy is less than if the wavefront is measured directly. This paper discusses and compares various aspheric optics testing schemes. Null tests that are discussed include the use of real and computer-generated holograms and the use of refractive and reflective null optics. Non-null tests that are discussed include lateral and radial shearing interferometry, direct phase measurement using large linear and two-dimensional solid-state detector arrays, sub-Nyquist interferometry, long-wavelength interferometry, and two-wavelength holography (or interferometry). The importance of combining lens analysis (design) software with interferogram analysis software is discussed.
''Theta gun,'' a multistage, coaxial, magnetic induction projectile accelerator (1985)

We experimentally and theoretically studied a multistage coaxial magnetic induction projectile accelerator. We call this system a ''theta gun'' to differentiate it from other coaxial accelerator concepts such as the mass driver. We conclude that this system can theoretically attain railgun performance only for large caliber or very high injection velocity and, even then, only for long coil geometry. Our experiments with a three-stage, capactor bank-driven accelerator are described. The experiments are modeled with a 1-1/2 dimensional equivalent circuit-hydrodynamics code which is also described. We derive an expression for the conditions of coaxial accelerator-railgun ''velocity breakeven'' in the absence of ohmic and hydrodynamic effects. This, in conjunction with an expression for the magnetic coupling coefficient, defines a set of geometric relations which the coaxial system must simultaneously satisfy. Conclusions concerning both the existence and configuration of a breakeven coaxial system follow from this requirement. The relative advantages and disadvantages of the coaxial induction projectile accelerator, previously cited in the literature, are critiqued from the viewpoint of our analysis and experimental results. We find that the advantages vis-a-vis the railgun have been overstated. 13 refs., 17 figs.
Oriental hornet venom enhances wound healing and repair in rat skin, possibly through its collagenolytic activity. (1983)

Oriental hornet (Vespa orientalis) venom sac extract (VSE) was topically applied to experimental wounds produced on the back skin of rats in order to observe histologically its effect on the healing process. In other studies the collagenolytic effect of VSE was investigated. The results clearly indicated that application of VSE enhanced the process of wound healing. Two weeks after wound induction a thick epidermis and maturation of the dermal connective tissue were seen in the experimental animals, whereas in the controls the dermis was thin and still showed granulation tissue, and the epidermis was thin. Incubation of VSE with purified neutral salt-soluble collagen (NSSC) labeled by reduction with [3H]NaBH4 brought about degradation of the substrate. It is assumed that VSE enhances the process of wound healing in the skin, probably due to its collagenolytic effect.
<i>Legionella</i> reduction after conversion to monochloramine for residual disinfection (2008)

Previous studies have shown that monochloramine disinfection of municipal water supplies is associated with decreased risk of healthcare‐associated Legionnaires— disease. A twoyear, prospective environmental study was conducted to determine whether converting from chlorine to monochloramine for water disinfection would decrease Legionella colonization of hot water systems. Water and biofilm samples were collected from 53 buildings. Prevalence ratios comparing Legionella colonization before and after monochloramine disinfection were adjusted for water system characteristics. Legionella colonized 60% of the hot water systems before monochloramine conversion versus 4% after conversion. The median number of colonized sites per building declined significantly with monochloramine disinfection. Increased prevalence of Legionella colonization was associated with water heater temperatures below 50oC, buildings taller than 10 stories, and interruptions in water service. Although no outbreaks of Legionnaires— disease were found, the study provides support that use of monochloramine in water supplies may reduce Legionella transmission and incidence of Legionnaires— disease.
Two-Photon Ionization of He through a Superposition of Higher Harmonics (2003)

We present experimental results and theoretical analysis of two-photon ionization of He by a superposition of the 7th to the 13th harmonic of a Ti:sapphire laser. Solving the time-dependent Schr\"odinger equation for He in a coherent polychromatic field, the ${\mathrm{H}\mathrm{e}}^{+}$ yield is calculated. From this yield the number of ${\mathrm{H}\mathrm{e}}^{+}$ ions produced has been estimated and found in reasonable agreement with its measured value. The present results establish the feasibility of a second-order autocorrelation measurement of superposition of harmonics, and thus they represent the precursor towards the direct temporal characterization of attosecond pulse trains.
Learning Face Age Progression: A Pyramid Architecture of GANs (2018)

The two underlying requirements of face age progression, i.e. aging accuracy and identity permanence, are not well studied in the literature. In this paper, we present a novel generative adversarial network based approach. It separately models the constraints for the intrinsic subject-specific characteristics and the age-specific facial changes with respect to the elapsed time, ensuring that the generated faces present desired aging effects while simultaneously keeping personalized properties stable. Further, to generate more lifelike facial details, high-level age-specific features conveyed by the synthesized face are estimated by a pyramidal adversarial discriminator at multiple scales, which simulates the aging effects in a finer manner. The proposed method is applicable to diverse face samples in the presence of variations in pose, expression, makeup, etc., and remarkably vivid aging effects are achieved. Both visual fidelity and quantitative evaluations show that the approach advances the state-of-the-art.
Stimulation of DNA Glycosylase Activities by XPC Protein Complex: Roles of Protein‐Protein Interactions (2010)

We showed that XPC complex, which is a DNA damage detector for nucleotide excision repair, stimulates activity of thymine DNA glycosylase (TDG) that initiates base excision repair. XPC appeared to facilitate the enzymatic turnover of TDG by promoting displacement from its own product abasic site, although the precise mechanism underlying this stimulation has not been clarified. Here we show that XPC has only marginal effects on the activity of E. coli TDG homolog (EcMUG), which remains bound to the abasic site like human TDG but does not significantly interacts with XPC. On the contrary, XPC significantly stimulates the activities of sumoylated TDG and SMUG1, both of which exhibit quite different enzymatic kinetics from unmodified TDG but interact with XPC. These results point to importance of physical interactions for stimulation of DNA glycosylases by XPC and have implications in the molecular mechanisms underlying mutagenesis and carcinogenesis in XP-C patients.
How convolutional neural networks see the world --- A survey of convolutional neural network visualization methods (2018)

Nowadays, the Convolutional Neural Networks (CNNs) have achieved impressive performance on many computer vision related tasks, such as object detection, image recognition, image retrieval, etc. These achievements benefit from the CNNs' outstanding capability to learn the input features with deep layers of neuron structures and iterative training process. However, these learned features are hard to identify and interpret from a human vision perspective, causing a lack of understanding of the CNNs' internal working mechanism. To improve the CNN interpretability, the CNN visualization is well utilized as a qualitative analysis method, which translates the internal features into visually perceptible patterns. And many CNN visualization works have been proposed in the literature to interpret the CNN in perspectives of network structure, operation, and semantic concept.In this paper, we expect to provide a comprehensive survey of several representative CNN visualization methods, including Activation Maximization, Network Inversion, Deconvolutional Neural Networks (DeconvNet), and Network Dissection based visualization. These methods are presented in terms of motivations, algorithms, and experiment results. Based on these visualization methods, we also discuss their practical applications to demonstrate the significance of the CNN interpretability in areas of network design, optimization, security enhancement, etc.
Field Validation of Swab Effects While Tripping-In the Hole on Deep, High Temperature Wells (1998)

Abstract In an earlier paper by the same authors (Kicks Caused by Tripping-In the Hole on Deep, High Temperature Wells), it was suggested that a combination of high temperature and high trip-in speeds could result in a secondary swab effect large enough to cause underbalance and subsequent well control incidents. Field validation of the earlier work is reported in this paper. A deep, high temperature well, similar to the ones discussed in the previous paper was chosen for the field validation. Field measurements of pressure, temperature and trip speeds were taken while tripping in the hole. The experimental procedures, data gathering, and analysis are described in this paper. Field data were compared to the predictions of a swab-surge model and remarkable agreement was found. The secondary swab effect was clearly measurable, and its magnitude compared very favorably with the model predictions. This increases the confidence in model results and the concept that kicks can result from tripping in the hole at high velocities. It is concluded that secondary swabs while tripping-in is an important design consideration for deep, high temperature wells. Underbalanced conditions can occur if the trip speeds are high, and if the mud weight is not compensated for the effects of high downhole temperature. Swab-surge models similar to the one used in this study can be used in the design phase to avoid kicks while tripping-in by determining maximum trip-in velocities and the effect of temperature and pressure on the effective density of the drilling fluid. P. 835
Characterization of Benzoquinone−Peptide Adducts by Electrospray Mass Spectrometry (2000)

Benzoquinone adducts were prepared with model peptides to identify characteristic features of adduct fragmentation in tandem mass spectrometry (MS) experiments. Model peptides contained cysteine and had a molecular mass of less than 2 kDa to facilitate peptide fragmentation in tandem MS analyses. Peptides were adducted with an excess of benzoquinone, and the adducts were analyzed by LC/MS. Adducts were identified by addition of 108 Da to the monoisotopic mass of the peptide, except in the case of oxytocin, which formed a bis adduct with addition of 216 Da. Tandem MS experiments were performed on the [M + 2H](2+) ions and/or the [M + H](+) ions. Sequence information obtained from modified peptides was comparable to that of their unmodified counterparts. A unique ion pair separated by 141 or 142 Da corresponding to beta-elimination of benzoquinol-S or benzoquinol-SH from a b(n) or y(n) series ion indicated attachment at the sulfur of the cysteine residue. An alternate ion pair of 211 Da corresponded to fragmentation at the peptide bond on either side of the adducted cysteine. Enzymatic digestion of BSA and a 2560 Da frog peptide with trypsin yielded tryptic peptides, which were treated with benzoquinone. In addition to ion pairs of 142 and 211 Da, singly and doubly charged tryptic peptide adducts showed a neutral loss of 142 Da from the precursor. Either one or both ion pairs were present in more than half of all the peptides that were examined. The neutral loss of 142 Da was present in all singly charged tryptic peptide adducts and in 11 out of 14 doubly charged tryptic peptide adducts. The data indicate that reliable detection of benzoquinone-cysteinyl peptide adducts requires monitoring of multiple spectral characteristics.
A structured approach to redundant disk array implementation (1996)

Error recovery in redundant disk arrays is typically performed in an ad hoc fashion, requiring architecture-specific code which limits extensibility and is difficult to verify. In this paper, we describe a technique for automating the execution of redundant disk array operations, including recovery from errors, independent of array architecture. Our approach employs a graphical representation of array operations and a two-phase error recovery scheme we refer to as roll-away error recovery. We demonstrate the validity of this approach in RAID-frame, a prototyping framework that separates architectural policy from execution mechanism. RAID-frame facilitates rapid prototyping of new RAID architectures by localizing modifications. In addition, RAID-frame implemented architectures run the same code when configured as an event-driven simulator, a user-level application managing raw disks, and as a Digital Unix device-driver capable of mounting a filesystem. Evaluation shows that RAID-frame performance is equivalent to less complex array implementations and that case studies of RAID levels 0, 1, 4, 5, 6, and parity declustering achieve expected performance.
RNA stimulates aggregation of microtubule‐associated protein tau into Alzheimer‐like paired helical filaments (1996)

The microtubule-associated protein tau is the main component of the paired helical filaments (PHFs) of Alzheimer's disease, the most common senile dementia. To understand the origin of tau's abnormal assembly we have studied the influence of other cytosolic components. Here we report that PHF assembly is strongly enhanced by RNA. The RNA-induced assembly of PHFs is dependent on the formation of intermolecular disulfide bridges involving Cys322 in the third repeat of tau, and it includes the dimerization of tau as an early intermediate. Three-repeat constructs polymerize most efficiently, two repeat constructs are the minimum number required for assembly, and even all six full-length isoforms of tau can be induced to form PHFs by RNA.
An evaluation of keyword, string similarity and very shallow syntactic matching for a university admissions processing infobot (2013)

?Infobots? are small-scale natural language question answering systems drawing inspiration from ELIZA-type systems. Their key distinguishing feature is the extraction of meaning from users? queries without the use of syntactic or semantic representations. Three approaches to identifying the users? intended meanings were investigated: keyword based systems, Jaro-based string similarity algorithms and matching based on very shallow syntactic analysis. These were measured against a corpus of queries contributed by users of aWWW-hosted infobot for responding to questions about applications to MSc courses. The most effective system was Jaro with stemmed input (78.57%). It also was able to process ungrammatical input and offer scalability.
PGC-1alpha Down-Regulation Affects the Antioxidant Response in Friedreich's Ataxia (2010)

PGC-1alpha down-regulation is likely to contribute to the blunted antioxidant response observed in cells from FRDA patients. This response can be restored by AMPK and PPARgamma agonists, suggesting a potential therapeutic approach for FRDA.
Risk Analysis of Trojan-Horse Attacks on Practical Quantum Key Distribution Systems (2014)

An eavesdropper Eve may probe a quantum key distribution (QKD) system by sending a bright pulse from the quantum channel into the system and analyzing the back-reflected pulses. Such Trojan-horse attacks can breach the security of the QKD system, if appropriate safeguards are not installed or if they can be fooled by the Eve. We present a risk analysis of such attacks based on extensive spectral measurements, such as transmittance, reflectivity, and detection sensitivity of some critical components used in a typical QKD systems. Our results indicate the existence of wavelength regimes, where the attacker gains considerable advantage as compared to launching an attack at 1550 nm. We also propose countermeasures to reduce the risk of such attacks.