gebhart/patrepeval huggingface dataset:
Direct detection of HSulf-1 and HSulf-2 activities on extracellular heparan sulfate and their inhibition by PI-88 (2009)

Heparan sulfates (HS) bind a diversity of protein ligands on the cell surface and in the extracellular matrix and thus can modulate cell signaling. The state of sulfation in glucosamines and uronic acids within the chains strongly influences their binding. We have previously cloned and characterized two human extracellular endoglucosamine 6-sulfatases, HSulf-1 and HSulf-2, which selectively liberate the 6-O sulfate groups on glucosamines present in N, 6-O, and 2-O trisulfated disaccharides of intact HS and heparins. These enzymes serve important roles in development and are upregulated in a number of cancers. To determine whether the Sulfs act on the trisulfated disaccharides that exist on the cell surface, we expressed HSulfs in cultured cells and performed a flow cytometric analysis with the RB4CD12, an anti-HS antibody that recognizes N- and O-sulfated HS saccharides. The endogenously expressed level of the cell surface RB4CD12 epitope was greatly diminished in CHO, HEK293, and HeLa cells transfected with HSulf-1 or HSulf-2 cDNA. In correspondence with the RB4CD12 finding, the N, 6-O, and 2-O trisulfated disaccharides of the HS isolated from the cell surface/extracellular matrix were dramatically reduced in the Sulf-expressed HEK293 cells. We then developed an ELISA and confirmed that the RB4CD12 epitope in immobilized heparin was degraded by purified recombinant HSulf-1 and HSulf-2, and conditioned medium (CM) of MCF-7 breast carcinoma cells, which contain a native form of HSulf-2. Furthermore, HSulf-1 and HSulf-2 exerted activity against the epitope expressed on microvessels of mouse brains. Both HSulf activities were potently inhibited by PI-88, a sulfated heparin mimetic with anti-cancer activities. These findings provide new strategies for monitoring the extracellular remodeling of HS by Sulfs during normal and pathophysiological processes.
Synthesis of 1-.BETA.-D-(5-Deoxy-5-iodoarabinofuranosyl)-2-nitroimidazole (.BETA.-IAZA): A Novel Marker of Tissue Hypoxia. (2003)

The present work describes the synthesis of the beta-isomer of 1-alpha-D-(5-deoxy-5-iodoarabinofuranosyl)-2-nitroimidazole (IAZA). Radioiodinated IAZA ((123)I-IAZA) has been extensively studied as a radiopharmaceutical for the diagnosis of regional and/or focal tissue hypoxia in a variety of clinical pathologies. The beta-anomer of IAZA, 1-beta-D-(5-deoxy-5-iodoarabinofuranosyl)-2-nitroimidazole (beta-IAZA, 1), was synthesized via an unconventional route starting from 1-beta-D-(ribofuranosyl)-2-nitroimidazole (AZR), with a change of configuration at the C-2'-position to afford 1-beta-D-(arabinofuranosyl)-2-nitroimidazole (beta-AZA, 7). Nucleophilic iodination of the 5'-O-toluenesulfonyl-2',3'-di-O-acetyl precursor of beta-AZA, 9, followed by deprotection, afforded 1 in satisfactory yield. beta-IAZA (1) was also synthesized from 7 using molecular iodine and triphenylphosphine.
ChemInform Abstract: PHOTOPHYSICAL STUDIES OF URANYL COMPLEXES. 4. X‐RAY PHOTOELECTRON AND LUMINESCENCE STUDIES OF HYDROLYZED URANYL SALTS (1984)

Abstract Die untersuchten festen Hydrolyseprodukte resultierten aus der langsamen, tropfenweisen Zugabe wäßriger l.0 M‐Lösungen von NaOH oder NH 4 OH zu gerührten Lösungen von 0.1 oder 1.0 M Uranylchlorid, ‐nitrat oder ‐acetal.
Learning Structural Edits via Incremental Tree Transformations (2021)

While most neural generative models generate outputs in a single pass, the human creative process is usually one of iterative building and refinement. Recent work has proposed models of editing processes, but these mostly focus on editing sequential data and/or only model a single editing pass. In this paper, we present a generic model for incremental editing of structured data (i.e., "structural edits"). Particularly, we focus on tree-structured data, taking abstract syntax trees of computer programs as our canonical example. Our editor learns to iteratively generate tree edits (e.g., deleting or adding a subtree) and applies them to the partially edited data, thereby the entire editing process can be formulated as consecutive, incremental tree transformations. To show the unique benefits of modeling tree edits directly, we further propose a novel edit encoder for learning to represent edits, as well as an imitation learning method that allows the editor to be more robust. We evaluate our proposed editor on two source code edit datasets, where results show that, with the proposed edit encoder, our editor significantly improves accuracy over previous approaches that generate the edited program directly in one pass. Finally, we demonstrate that training our editor to imitate experts and correct its mistakes dynamically can further improve its performance.
Another specific effect of prenatal acetazolamide exposure in the mouse (1983)

Abstract Subcutaneous injection of pregnant mice on day 8 of gestation with 1,000 mg/kg or 200 mg/kg of an aqueous solution of the sodium salt of acetazolamide, divided into three equal treatments at 8‐hour intervals, in two series of experiments performed 8 months apart on separately purchased random bred CD‐1 animals, resulted in the occurrence of a novel variant of the frontal bones of the skull when animals exposed in utero were examined at 62 ± 2 days postnatal. In its greatest manifestation this variation consisted of a 2–3 mm posteriad extension of the dorsomedial portion of the posterior margin of both bones, although all degrees of asymmetry and variations in the extent of involvement of the posterior margin of the bones were seen. This frontal extension variant was seen in 30.9 ± 4.7% and 53.1 ± 5.0% of the 97 and 98 specimens in the highdose groups, and in 8.1 ± 2.7% and 14.6 ± 3.7% of the 99 and 89 low‐dose specimens in the two series. It was not seen in untreated groups, or to any significant extent in vehicle‐treated groups, or in a treatment regime involving exposure during days 9–11 of gestation. It was also not seen in 2,110 specimens from four other series of experiments reported in detail involving the teratogens, trypan blue (two series), 5‐bromodeoxyuridine, or 2,4,5‐T, or in approximately 1,000 specimens from comparable experiments with a variety of pesticides (Maneb, Captan, Trifluralin, Decamethrin) or Thalidomide. In contrast, a morphologically analogous variant, accessory parietal, in which a suture in the anterodorsal surface of the parietal bones running posteromedial and seemingly delimiting a separate bone, is seen in all series. Although it looks as though frontal extension could be an accessory parietal fused with the frontal bone, observation of the specimens does not strongly support that relationship. Even if that were the case, it happens only in day‐8 acetazolamide exposure. From the rather extensive series of observations performed, it would appear that frontal extension is a specific response to in utero exposure to acetazolamide during the day 8 of gestation.
Simple switching control method changes power converter into a current source (1978)

A switching converter with an LC output filter behaves as a loose-tolerance voltage-controlled current source if each switch closure is ended when switch current reaches an adjustable threshold. This converter is then combined with an external feedback to produce a precise output voltage. By generating a fixed voltage with a current source in this manner, the converter has many advantages including continuous protection of the switches, stable and equal load sharing when several converters are operated in parallel, inherent overload protection, automatic switch symmetry correction, and fast system response.
Iron Maiden While Jogging, Debussy for Dinner? - An Analysis of Music Listening Behavior in Context. (2015)

Abstract. Contextual information of the listener is only slowly being integrated into music retrieval and recommendation systems. Given the enormous rise in mobile music consumption and the many sensors inte-grated into today’s smart-phones, at the same time, an unprecedented source for user context data of different kinds is becoming available. Equipped with a smart-phone application, which had been developed to monitor contextual aspects of users when listening to music, we collected contextual data of listening events for 48 users. About 100 different user features, in addition to music meta-data have been recorded. In this paper, we analyze the relationship between aspects of the user context and music listening preference. The goals are to assess (i) whether user context factors allow predicting the song, artist, mood, or genre of a listened track, and (ii) which contextual aspects are most promising for an accurate prediction. To this end, we investigate various classifiers to learn relations between user context aspects and music meta-data. We show that the user context allows to predict artist and genre to some extent, but can hardly be used for song or mood prediction. Our study further reveals that the level of listening activity has little influence on the accuracy of predictions. 1
Intracavity coherent beam combining of 21 semiconductor gain elements using SPGD* (2012)

Coherent beam combining (CBC) allows for achieving high output power in a single diffraction limited beam. Here we report on intracavity CBC of 21-element semiconductor array with 81% beam combining efficiency out of a system maximum combining efficiency of 90%.
Program challenges directional survey accuracy claims (1984)

Directional instrument accuracy depends on where the instruments are used. Claims of absolute accuracy, made regardless of well location or geometry, are questionable. Eastman Whipstock has developed a computer program which demonstrates that: accuracy depends not only on latitude, but also on longitude and borehole orientation; tools that meet tight specs in Houston may not perform as well in the North Sea or Alaska; and that current accuracy specifications are over-simplified and thus unrealistic. The new program takes into account a number of previously unconsidered factors that can affect tool accuracy, and will help operators evaluate surveying instruments according to their particular requirements.
A parallel Ant Colony System based on region decomposition for Taxi-Passenger Matching (2017)

Taxi dispatch is a critical issue for taxi company to consider in modern life. This paper formulates the problem into a taxi-passenger matching model and proposes a parallel ant colony optimization algorithm to optimize the model. As the search space is large, we develop a region-dependent decomposition strategy to divide and conquer the problem. To keep the global performance, a critical region is defined to deal with the communications and interactions between the subregions. The experimental results verify that the proposed algorithm is effective, efficient, and extensible, which outperforms the traditional global perspective greedy algorithm in terms of both accuracy and efficiency.
Forecasting driving behavior to enable efficient grid integration of plug-in electric vehicles (2012)

In this paper, we evaluate a time series based method for predicting the first daily departure time (FDDT) of commuter vehicles. This task is relevant for the grid integration of plug-in electric vehicles (PEVs), since it allows for actively managing their electricity demand during the connection interval. Our study is based on a sample of 445 vehicle usage traces which were collected in the Puget Sound Traffic Choices Study using the Global Positioning System (GPS). We advance knowledge in the area of vehicle usage prediction in a smart grid context in four ways: First, we propose a method for selecting variable size subsets of vehicle usage traces that are more predictable irrespective of the concrete forecasting method used. Second, we show that FDDTs should not be modeled with basic. Third, we compare a number of time series based forecasting models using the mean absolute deviation (MAD) and forecast availability to identify a model with high forecasting accuracy and high forecast availability. Fourth, we report empirical confidence intervals to demonstrate the performance of our approach and discuss implications with respect to using PEVs for demand side management. A major finding of this work is that, even for commuters, FDDTs are hard to predict using historical realizations alone. However, the forecasting accuracy varies a lot from vehicle to vehicle and weekday to weekday. Moreover, forecasting errors are skewed in a way that facilitates non-disruptive charging control but may limit load shifting potential. Finally, using the example of ex-ante knowledge about workdays, we show that further potential for improvement lies in considering more data sources.
GSM network signaling (1997)

GSM is a wireless digital signaling network standard designed by standardization committees from the major European telecommunications operators and manufacturers. This article introduces the software platform for GSM network signaling protocol called Mobile Application Part (MAP). We describe the MAP services, the MAP protocol machine, the MAP dialog model, and then illustrate the MAP specific service primitives by an example.
ErbB/HER pathway profiling in formalin-fixed paraffin embedded tissues using multiplexed proximity-based assays (2005)

645 Background: The EGFR, ErbB2, ErbB3 and ErbB4 are members of the Type I receptor tyrosine receptor kinase family (also known as the HER or ErbB family). Overexpression of these receptors in a number of cancer types (e.g. breast, colon, ovarian, and lung) results in an aggressive phenotype with poor prognosis. However, clinical trial data has shown that overexpression of ErbB receptors alone is not sufficient to predict patient response. A thorough analysis of the activation status of the ErbB pathway will likely achieve better prognosis. Methods: We report the development of a novel proximity-based, multiplexed assay to detect and quantify the levels of EGFR/EGFR, EGFR/HER2, HER2/HER2, HER2/HER3, and EGFR/HER3 homo- and hetero-dimers in formalin-fixed, paraffin embedded (FFPE) samples of tumor tissues including breast, lung, ovarian, head and neck, and colon cancers. The eTag assay is performed on samples that are deparaffinized, rehydrated and processed by standard protocols. Cytokeratin is used as an internal reference control for the total epithelial content. Upon completion of the assay the reporter eTags are released and separated by capillary gel electrophoresis and quantified by eTag-Informer software. Results: The data demonstrated the simultaneous detection and quantification of HER receptor expression, dimerization and phosphorylation in a single tissue section. The validity of the detection and quantification of HER dimers in FFPE tissue samples was independently confirmed by immunoprecipitation/Western blot and eTag assays in total cell lysates from the same tissues. Conclusion: We conclude that the eTag assays provide sensitive, quantitative assessment of various HER dimers from the same sample. They can be used to determine the activation status of ErbB/HER receptor in clinical sample for the correlation with disease prognosis or response to targeted therapies. No significant financial relationships to disclose.
Universal Negative Poisson Ratio of Self-Avoiding Fixed-Connectivity Membranes (2001)

We determine the Poisson ratio of self-avoiding fixed-connectivity membranes, modeled as impenetrable plaquettes, to be sigma = -0.37(6), in statistical agreement with the Poisson ratio of phantom fixed-connectivity membranes sigma = -0.32(4). Together with the equality of critical exponents, this result implies a unique universality class for fixed-connectivity membranes. Our findings thus establish that physical fixed-connectivity membranes provide a wide class of auxetic (negative Poisson ratio) materials with significant potential applications in materials science.
Neurotoxic Aβ peptides increase oxidative stress <i>in vivo</i> through NMDA‐receptor and nitric‐oxide‐synthase mechanisms, and inhibit complex IV activity and induce a mitochondrial permeability transition <i>in vitro</i> (2001)

Beta amyloid (Abeta) peptides accumulate in Alzheimer's disease and are neurotoxic possibly through the production of oxygen free radicals. Using brain microdialysis we characterized the ability of Abeta to increase oxygen radical production in vivo. The 1-40 Abeta fragment increased 2,3-dehydroxybenzoic acid efflux more than the 1-28 fragment, in a manner dependent on nitric oxide synthase and NMDA receptor channels. We then examined the effects of Abeta peptides on mitochondrial function in vitro. Induction of the mitochondrial permeability transition in isolated rat liver mitochondria by Abeta(25-35) and Abeta(35-25) exhibited dose dependency and required calcium and phosphate. Cyclosporin A prevented the transition as did ruthenium red, chlorpromazine, or N-ethylmaleimide. ADP and magnesium delayed the onset of mitochondrial permeability transition. Electron microscopy confirmed the presence of Abeta aggregates and swollen mitochondria and preservation of mitochondrial structure by inhibitors of mitochondrial permeability transition. Cytochrome c oxidase (COX) activity was selectively inhibited by Abeta(25-35) but not by Abeta(35-25). Neurotoxic Abeta peptide can increase oxidative stress in vivo through mechanisms involving NMDA receptors and nitric oxide sythase. Increased intracellular Abeta levels can further exacerbate the genetically driven complex IV defect in sporadic Alzheimer's disease and may precipitate mitochondrial permeability transition opening. In combination, our results provide potential mechanisms to support the feed-forward hypothesis of Abeta neurotoxicity.
Ultrafast and scalable cone‐beam CT reconstruction using MapReduce in a cloud computing environment (2011)

An ultrafast, reliable and scalable 4D CBCT∕CT reconstruction method was developed using the MapReduce framework. Unlike other parallel computing approaches, the parallelization and speedup required little modification of the original reconstruction code. MapReduce provides an efficient and fault tolerant means of solving large-scale computing problems in a cloud computing environment.
High commitment management and unionization in the UK (1996)

High commitment management, as popularized by Walton and Lawler, and trade unionism are often thought of as antithetical. The research reported here uses an index of high commitment developed by the author to assess whether indeed this is the case, or whether they do in fact co-exist, as is increasingly being acknowledged in the UK as possible. Using data from a sample of 135 manufacturing plants in the UK, the paper shows that, whilst the use of high commitment management did increase in the late 1980s, it was not more likely to be practised in the non-unionized ones. Furthermore, unionism did not seem incompatible with relatively high levels of high commitment management. Nonetheless, the rate of change of HCM between 1986 and 1990 was lower in plants with recognized trade unions, which suggests that unions have a dragging effect on HCM, but will not affect its ultimate extent. The research also demonstrates that the co-existence of unionism and high commitment management cannot be put down to managements’adopting HCM in a fragmented or ad hoc way, nor does it appear to be mediated by the state of the labour market.
Advanced boiling water reactor, the next generation-status and future (2002)

The advanced boiling water reactor (ABWR) is an advanced water reactor designed by an international team of engineers and designers to address the utility and public needs for the next generation of power plants. The major emphasis in the design of the plant has been on improved operability and maintainability. This has led to an overall plant design that is simpler to build, maintain, and operate and at the same time has significantly enhanced safety features, including several features that are inherent to BWR designs and ensure 'passive' responses to transients and accidents. The author also discusses other key features of the ABWR: internal recirculation pumps, fine motion control rod drives, digital control and instrumentation, multiplexed fiber optic cabling network, pressure suppression containment, structural integration of the containment and reactor building, and advanced turbine/generator with 52-in last stage buckets. The 1356 MWe ABWR design is being applied as a two unit project by the Tokyo Electric Power Co. Inc., at its Kashiwazaki-Kariwa site in Japan. Construction began September 1991 and commercial operation is scheduled for 1996, with the second unit one year later.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The cellulosomes from <i>Clostridium cellulolyticum</i> (2009)

Cellulosomes produced by Clostridium cellulolyticum grown on cellulose were purified and separated using anion-exchange chromatography. SDS/PAGE analysis of six fractions showed variations in their cellulosomal protein composition. Hydrolytic activity on carboxymethyl cellulose, xylan, crystalline cellulose and hatched straw differed from one fraction to another. Fraction F1 showed a high level of activity on xylan, whereas fractions F5 and F6 were most active on crystalline cellulose and carboxymethyl cellulose, respectively. Several cellulosomal components specific to fractions F1, F5 and F6 were investigated using MS analysis. Several hemicellulases were identified, including three xylanases in F1, and several cellulases belonging to glycoside hydrolase families 9 and 5 and, a cystein protease inhibitor were identified in F5 and F6. Synergies were observed when two or three fractions were combined. A mixture containing fractions F1, F3 and F6 showed the most divergent cellulosomal composition, the most synergistic effects and the highest level of activity on straw (the most heterogeneous substrate tested). These findings show that on complex substrates such as straw, synergies occur between differently composed cellulosomes and the degradation efficiency of the cellulosomes is correlated with their enzyme diversity.
Immune stimulation in the silkworm, <i>Bombyx mori</i> L., by CpG oligodeoxynucleotides (2003)

Synthetic ODNs containing unmethylated CpG dinucleotides are known to stimulate immune responses in vertebrates, but so far the effect has not been studied in insects. In this report, we describe an induction of immune response following injection of oligodeoxynucleotides (ODNs) into the insect hemocoel. The fifth instar silkworm (Bombyx mori L.) larvae were injected with several synthetic ODNs containing variable number of unmethylated CpG motifs, heat-denatured genomic DNA of B. mori itself, or intact genomic DNA to observe a new induction pattern in the insect immune mechanism. When the induction of immune response was examined based on the expression rates of genes for antibacterial peptides such as attacin and cecropin, we could confirm that it was triggered upon injection of ODNs. The expression was, however, neither dependent on numbers of CpG motifs nor methylation of CpGs in ODNs. Furthermore, it was confirmed that the presence of CpG in ODN was not involved in the induction pattern of insect immunity caused by ODNs, although it has been reported that vertebrates respond in a specific manner against invading ODNs containing CpG dinucleotides. In addition, insect immunity was not stimulated by injection of intact DNA from host. In contrast, the injection of denatured genomic DNA provoked the host immune reaction. Taken together, our data suggest that foreignness of ODNs or DNA might be a key factor in the induction of insect immunity.