gebhart/patrepeval huggingface dataset:
WikiPathways: building research communities on biological pathways (2011)

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further.
Creativity and Artificial Intelligence (2007)

Creativity and Artificial Intelligence: A Conceptual Blending Approach takes readers into a computationally plausible model of creativity. Inspired by a thorough analysis of work on creativity from the areas of philosophy, psychology, cognitive science, cognitive linguistics and artificial intelligence, the author deals with the various processes, principles and representations that lie underneath the act of creativity. Focusing on Arthur Koestler's Bisociations , which eventually lead to Turner and Fauconnier's conceptual blending framework, the book proposes a theoretical model that considers blends and their emergent structure as a fundamental cognitive mechanism. The author thus discusses the computational implementation of several aspects of conceptual blending theory, namely composition, completion, elaboration, frames and optimality constraints. Informal descriptions and examples are supplied to provide non-computer scientists as well as non-cognitive linguists with clear insights into these ideas. Several experiments are made, and their results are discussed, with particular emphasis on the validation of the creativity and conceptual blending aspects. Written by a researcher with a background in artificial intelligence, the book is the result of several years of exploration and discussion from different theoretical perspectives. As a result, the book echoes some of the criticism made on conceptual blending and creativity in artificial intelligence, and thus proposes improvements in both areas, with the aim of being a constructive contribution to these very intriguing, yet appealing, research orientations.
Growth of the Maize Primary Root at Low Water Potentials (1988)

Seedlings of maize (Zea mays L. cv WF9 x Mo 17) were grown in vermiculite at various water potentials. The primary root continued slow rates of elongation at water potentials which completely inhibited shoot growth. To gain an increased understanding of the root growth response, we examined the spatial distribution of growth at various water potentials. Time lapse photography of the growth of marked roots revealed that inhibition of root elongation at low water potentials was not explained by a proportional decrease in growth along the length of the growing zone. Instead, longitudinal growth was insensitive to water potentials as low as - 1.6 megapascal close to the root apex, but was inhibited increasingly in more basal locations such that the length of the growing zone decreased progressively as the water potential decreased. Cessation of longitudinal growth occurred in tissue of approximately the same age regardless of spatial location or water status, however. Roots growing at low water potentials were also thinner, and analysis revealed that radial growth rates were decreased throughout the elongation zone, resulting in greatly decreased rates of volume expansion.
Systematic construction of anomaly detection benchmarks from real data (2013)

Research in anomaly detection suffers from a lack of realistic and publicly-available problem sets. This paper discusses what properties such problem sets should possess. It then introduces a methodology for transforming existing classification data sets into ground-truthed benchmark data sets for anomaly detection. The methodology produces data sets that vary along three important dimensions: (a) point difficulty, (b) relative frequency of anomalies, and (c) clusteredness. We apply our generated datasets to benchmark several popular anomaly detection algorithms under a range of different conditions.
Re-evaluation of absorbed fractions for photons and electrons in spheres of various sizes. (2000)

Absorbed fractions for unit density spheres in an infinite unit density medium, previously calculated for photon emitters and electron emitters, were reevaluated with the Monte Carlo codes EGS4 and MCNP4B.Activity was assumed to be distributed uniformly throughout the spheres, and absorbed fractions for self-irradiation were calculated at discrete photon and electron energies.For electrons, the codes were in very good agreement with each other (+/-5%) and with published values, except at higher energies in the very smallest spheres, where some differences exceeded 10%. For photons, the codes were again in good agreement with each other but produced results that varied considerably from published MIRD values. For energies <1 MeV and sphere sizes <50 g, the absorbed fractions determined using the Monte Carlo codes were typically 20%-40% higher than values in MIRD 3 and 8. For energies >1 MeV, the Monte Carlo values were sometimes lower than those in the MIRD documents. Recommended values, generally the average results from the 2 Monte Carlo codes, are given for all sphere sizes and energies for both electrons and photons.The absorbed fractions calculated using the Monte Carlo codes should replace the older values and are helpful in evaluating tumor doses, doses to small organs, and other situations in which a uniform distribution of activity throughout a spherical structure of unit density can be assumed.
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures (2008)

LC-MS/MS has emerged as the method of choice for the identification and quantification of protein sample mixtures. For very complex samples such as complete proteomes, the most commonly used LC-MS/MS method, data-dependent acquisition (DDA) precursor selection, is of limited utility. The limited scan speed of current mass spectrometers along with the highly redundant selection of the most intense precursor ions generates a bias in the pool of identified proteins toward those of higher abundance. A directed LC-MS/MS approach that alleviates the limitations of DDA precursor ion selection by decoupling peak detection and sequencing of selected precursor ions is presented. In the first stage of the strategy, all detectable peptide ion signals are extracted from high resolution LC-MS feature maps or aligned sets of feature maps. The selected features or a subset thereof are subsequently sequenced in sequential, non-redundant directed LC-MS/MS experiments, and the MS/MS data are mapped back to the original LC-MS feature map in a fully automated manner. The strategy, implemented on an LTQ-FT MS platform, allowed the specific sequencing of 2,000 features per analysis and enabled the identification of more than 1,600 phosphorylation sites using a single reversed phase separation dimension without the need for time-consuming prefractionation steps. Compared with conventional DDA LC-MS/MS experiments, a substantially higher number of peptides could be identified from a sample, and this increase was more pronounced for low intensity precursor ions.
Storage protein changes during zygotic embryogenesis in interior spruce (1991)

The major storage proteins isolated from protein bodies of embryo tissues of interior spruce Picea glauca (Moench) Voss/Picea engelmanii Parry had apparent molecular weights of 41, 35, 33, 24 and 22 kD. Minor proteins of 30 and 27.5 kD were also observed. Based on their solubility characteristics, the 41 kD protein was identified as a water and buffer-soluble albumin, and the 35, 33, 24 and 22 kD proteins were characterized as buffer-insoluble, high salt-soluble globulins. Two-dimensional electrophoresis revealed each protein was composed of several isoelectric variants. Developmentally specific accumulation of storage proteins was observed during embryogenesis. The 41 kD protein only accumulated during the later stages of cotyledon maturation, whereas the other storage proteins began to accumulate during the early stages of embryo development. All storage proteins showed major accumulations during cotyledon maturation.
Algorithm 938 (2014)

Data sequences generated by on-line sensors can become arbitrarily large and must, therefore, be pared down to fit into available memory. For situations where only the most recent data is of interest, this problem can be solved with optimal efficiency by a simple circular buffer: it fills each memory location with useful data, and requires just one write to memory per update. The algorithm presented here provides essentially the same efficiency, but while maintaining a continuously updated, fixed-size, compressed representation of the entire data sequence. Each value in these compressed sequences represents a statistic (an average, maximum, random sample, etc.) computed over a contiguous chunk of the original sequence. Compressing circular buffers gain their efficiency by using an alternative indexing sequence, based on well-known principles of elementary number theory, to ensure that each newly written value gets stored in the unoccupied location created when the two oldest sequential over-sampled values are compressed into one. The associated Java implementation supports a variety of aggregating statistics and is used to compare the algorithm's performance with a more obvious approach (doubling).
Effect of gossypol on DNA synthesis and cell cycle progression of mammalian cells in vitro. (1984)

Gossypol, a yellow phenolic compound extracted from cotton plants that is being used as a male antifertility drug, has been found to have cytotoxic effects. The objective of the present study was to determine the cause of these cytotoxic effects in cultured cells and to ascertain whether cells in certain phases of the cell cycle were more sensitive to the drug than were cells in other phases. HeLa or Chinese hamster ovary cells were exposed to various concentrations of gossypol for varying periods of time, and the effects of the drug on the growth rate, cell cycle traverse, plating efficiency, and macromolecular synthesis were measured. The results of this study indicate that gossypol is a specific inhibitor of DNA synthesis; it has no effect on RNA and protein synthesis at a concentration of 10 micrograms/ml and hence has no effect on the cell cycle traverse of cells from G2 to the beginning of S phase. In the presence of the drug, cells can enter S phase but fail to complete replication. The effects of the drug on growth rate and plating efficiency indicate that there is a threshold concentration at which gossypol becomes effective as a cytotoxic agent. Gossypol did not increase chromosome aberrations in the treated cells. Since gossypol irreversibly blocks cells in S phase, it could be useful as an antitumor drug.
Nonvolatile memory devices based on organic field-effect transistors (2011)

Among the many possible device configurations for organic memory devices, organic field-effect transistor (OFET) memory is an emerging technology with the potential to realize lightweight, low-cost, flexible charge storage media. In this feature article, the recent progress in the classes of OFET-based memory, including floating gate OFET memory, polymer electret OFET memory, ferroelectric OFET memory and several other kinds of OFET memories with unique configurations, are introduced. Finally, the prospects and problems of OFETs memory are discussed.
Gene Therapy That Works (2013)

Gene therapy trials show a beneficial effect in children suffering from a neurodegenerative disorder or an immunodeficiency disease. [Also see Research Articles by Biffi et al. and Aiuti et al. ]
The quartz crystal microbalance; radial/polar dependence of mass sensitivity both on and off the electrodes (1990)

The response of AT-cut quartz crystal microbalances is analysed theoretically to show how mass sensitivity varies over the electroded and bare quartz areas. Analytical solutions are presented for the radial and polar dependence of mass sensitivity as a function of the electrode areal density for both planar and plano-convex crystals. In many surface science applications it is desirable to minimise the off-electrode sensitivity of the QCM, so as to make the fractional on-electrode response as close to unity as possible. This fractional response is shown to increase with the electrode mass, but to be in the range 0.90 to 0.94 for the planar crystals in common use. On the other hand, for plano-convex crystals this response readily exceeds 0.99. To check the accuracy of the calculations a simple method has been devised to deposit small dots of well defined mass at points on the crystal surface. These measurements show that the derived expressions for mass sensitivity are correct to within the measurement accuracy. The dots are deposited using a permanent marker pen giving a mass per dot of 0.21 mu g. After measurement, the dots are readily removed by solvent washing leaving the crystal calibrated and ready for other studies.
Behaviour, realism and immersion in games (2005)

Immersion is recognised as an important element of good games. However, it is not always clear what is meant by immersion. Earlier work has identified possible barriers to immersion including a lack of coherence between different aspects of the game. Building on this work, we designed an experiment to examine people's expectations of how a game should behave and what would happen if that behaviour was deliberately made to be incoherent. The idea then is to understand immersion through seeing how immersion can be broken. The main manipulation was to alter the behaviour and realism of the graphics in the course of a simple game situation. Surprisingly, results indicated that participants could be so immersed within a simple environment such that even significant changes in behaviour had little effect on the level of immersion. In some cases, the attempted disruptions went completely unnoticed. These results suggest that immersion within an application can overcome effects which are completely against user expectations.
An Explanation of Oscillations Due to Wind Power Plants Weak Grid Interconnection (2017)

An existing wind power plant at ERCOT experienced poorly damped and undamped voltage oscillations under weak grid conditions. The oscillations became worse during high power outputs. This letter aims to find the root cause of such oscillations. Our research provides a linearized system model by combining the vector control of wind power plants and the weak grid interconnection. Using this model, this letter succeeds in explaining that the weak grid condition introduces a zero in right half plane for the open-loop system, which can lead to poorly damped or undamped oscillations.
Inulin - A versatile polysaccharide with multiple pharmaceutical and food chemical uses (2015)

α-D-glucopyranosyl-[β-D-fructofuranosyl](n-1)-D-fructofuranoside, commonly referred to as inulin, is a natural plant-derived polysaccharide with a diverse range of food and pharmaceutical applications. It is used by the food industry as a soluble dietar
Chronic vulvovaginal candidiasis. (2001)

Frequently ignored by the medical community, chronic vulvovaginal symptoms are relatively common and can frustrating for patients and physicians. Establishing a proper diagnosis will lay the foundation for an effective therapeutic therapeutic plan. Fungal cultures are an important component of the work-up. The most common causes of chronic vaginal symptoms are recurrent vulvovaginal candidiasis (RVVC), vulvar vestibulitis syndrome and irritant dermatitis. In patients with RVVC caused by Candida albicans, host factors may play an important role. Long-term oral antifungal therapy will break the pattern of recurrence in many patients. Infections caused by other species of yeast may be more resistant to standard treatment approaches.
Friedländer condensation of 5-aminopyrazole-4-carbaldehydes with reactive α-methylene ketones: Synthesis of pyrazolo[3,4-<i>b</i>]pyridines (2005)

A series of 1,3,6-trisubstituted and 1,3,5,6-tetrasubstituted pyrazolo[3,4-b]pyridines 5 has been synthesized by Friedlander condensation of 5-arninopyrazole-4-carbaldehydes 3 with α-methylene ketones such as acetone (4a) or acetophenones 4b-f with potassium hydroxide as basic catalyst. Condensation of 5-aminopyrazole-4-carbaldehydes 3 and unsymmetric dialkylketones 6 yielded mixtures of isomeric pyra-zolo[3,4-b]pyridine derivatives 7 and 8. Condensation of 5-aminopyrazole-4-carbaldehydes 3 with CH-acidic acylacetonitriles 9 and acylacetates 11 with piperidine as basic catalyst yielded pyrazolo[3,4-b]pyri-dine-5-carbonitriles 10 and pyrazolo[3,4-b]pyridine-5-carboxylates 12; with diethyl malonate 13 as CH-acidic component, pyrazolo[3,4-b]pyridin-6-ones 14 were obtained.
Digital X-ray imaging (1987)

A brief rationale for the desirability of implementing digital X-ray imaging techniques is provided in the paper. The technology presently available or under development for actually producing digital X-ray data is described under two separate headings, namely: (a) imageintensifier/TV systems and (b) radiographic (filmreplacement) systems. The underlying design requirements for digital fluorography systems employing image-intensifier/TV systems is outlined. The flying spot, linear array, proximity-type intensifier, laser-scanned photostimulable phosphor and electrostatic processes are also discussed. Existing and future requirements for digital image display, data storage and processing are presented, and, finally, the potential impact on developments in medical imaging of introducing digital X-ray technology is indicated.
Structure of fumarate reductase on the cytoplasmic membrane of Escherichia coli (1983)

The terminal electron transfer enzyme fumarate reductase has been shown to be composed of a membrane-extrinsic catalytic dimer of 69- and 27-kilodalton (kd) subunits and a membrane-intrinsic anchor portion of 15- and 13-kd subunits. We prepared inverted membrane vesicles from a strain carrying the frd operon on a multicopy plasmid. When grown anaerobically on fumarate-containing medium, the membranes of this strain are highly enriched in fumarate reductase. When negatively stained preparations of these vesicles were examined with an electron microscope, they appeared to be covered with knob-like structures about 4 nm in diameter attached to the membrane by short stalks. Treatment of the membranes with chymotrypsin destroyed the 69-kd subunit, leaving the 27-, 15-, and 13-kd subunits bound to the membrane; these membranes appeared to retain remnants of the structure. Treatment of the membranes with 6 M urea removed the 69- and 27-kd subunits, leaving the anchor polypeptides intact. These vesicles appeared smooth and structureless. A functional four-subunit enzyme and the knob-like structure could be reconstituted by the addition of soluble catalytic subunits to the urea-stripped membranes. In addition to the vesicular structures, we observed unusual tubular structures which were covered with a helical array of fumarate reductase knobs.
Generation of an Anti-idiotypic Antibody as a Surrogate Ligand for Sulfamethazine in Immunoassay Procedures (2000)

Abstract We report the generation of an anti-idiotypic antibody, clone 12E12, against antisulfamethazine (SMZ) as a surrogate ligand for SMZ in immunoassay procedures. This has been achieved by using the primary monoclonal anti-SMZ antibody as an immunogen in hybridoma technology followed by screening of the resulting hybridromas for binding to the SMZ site of the primary anti-SMZ antibody. Characterization of a strong anti-idiotypic antibody of the betatype, clone 12E12, capable of mimicking SMZ, permitted the development of immunoassay formats for SMZ based on the idiotypic and anti-idiotypic approach and the direct measurement of SMZ content in diluted pig urine. The availability of the strong betatypic anti-idiotypic antibody acting as a surrogate ligand for SMZ enables antibodies to be labeled instead of ligands and offers interesting possibilities for the development of competitive type non-isotopic immunoassays for SMZ. Keywords: SulfamethazineAnti-IDIOTYPIC AntibodyImmunoassayTime-RESOLVED FluorescenceMonoclonal Antibody
Dynamic Self-Assembly and Patterns in Electrostatically Driven Granular Media (2003)

We show that granular media, consisting of metallic microparticles immersed in a poorly conducting liquid in a strong dc electric field, self-assemble into a rich variety of novel phases. These phases include static precipitates: honeycombs and Wigner crystals; and novel dynamic condensates: toroidal vortices and pulsating rings. The observed structures are explained by the interplay between charged granular gas and electrohydrodynamic convective flows in the liquid.
An Overview of Factors Influencing the Enzymatic Hydrolysis of Lignocellulosic Feedstocks (2000)

Lignocellulosic biomass conversion to ethanol promises to provide an environmentally benign alternative fuel that can reduce the consumption of gasoline, thereby reducing our dependence on a non-renewable energy source and improving the urban air quality. The process of microbial degradation of biomass is not understood at the molecular level and yet it is clear that many microorganisms have evolved diverse mechanisms to accomplish this task. We review current concepts regarding enzymatic hydrolysis of bioethanol feedstocks and point to technical challenges requiring further R&D.
Through-silicon-via built-in self-repair for aggressive 3D integration (2012)

Three-dimensional (3D) integration by die-/wafer-level stacking becomes a reality, as Through-Silicon-Via technologies emerge. However, poor reliability and yield of TSV interconnects remain major challenges of this promising technology. In this paper, we propose an efficient Built-In Self-Repair (TSV-BISR) strategy for TSV faults due to manufacturing and aging defects. After interconnect tests, we replace faulty TSVs with fault-free spares using shift operations. Among the benefits of this solution is that the self-repair signals are determined on-chip without any external intervention. Moreover, we show that with TSV-BISR better reparability is achieved with fewer spares than in existing TSV repair techniques. We also show that for 3D chips with interconnect reparability targets above 98% we reduce the area needed for spares and repair logic by up to 40%.
Generics, delegates and functional programming in C# 2.0 (2006)

Functions are first class objects in functional languages such as Scheme or ML - functions can be passed as parameters, functions can construct and return functions. The functional style of programming that this allows is quite distinct from the style normally used with languages such as Java, C or C++. Delegates in C# allow mimicking important features of functional programming in a rather different way than in Java [3]. C# 2.0 introduces features such as generic classes, generic delegates and anonymous methods which make functional programming even easier and more natural. Generic delegates and anonymous methods are used to model functional programming in C# 2.0. This allows the use of a functional programming style in C# and is a tool for exploring some of the interesting new features of C# from outside the box.