gebhart/patrepeval huggingface dataset:
Nearest neighbor analysis of heparin: identification and quantitation of the products formed by selective depolymerization procedures (1976)

Heparin was carboxyl-reduced with sodium boro[3H]hydride and converted to a mixture of oligosaccharides by treatment with nitrous acid at pH 2. The oligosaccharide mixture was aldehyde-reduced with sodium boro[3H]hydride and the mixture of products, labeled both in the hexoses formed in the carboxyl-reduction step and in the reducing sugars formed in the nitrous acid reaction, was separated and analyzed. The major product, L-idosyl 2-sulfate leads to anhydro-D-mannitol 6-sulfate (I), contained 60% of hexoses derived from the hexuronic acid residues in the original heparin. A second product, which contained 15% of the hexoses derived from the hexuronic acid residues in the original heparin, was identified as a tetrasaccharide composed of two L-idosyl 2-sulfate residues, one anhydro-D-mannitol 6-sulfate residue (the reducing end),and a hydroxymethylpentose sulfate residue formed by deamination of a disulfated D-glucosamine residue without bond cleavage. Several additional disaccharides derived from the regions of the polymer which contained D-glucuronic acid residues and lower degrees of O-sulfation were also identified among the deamination products. The oligosaccharides that were obtained accounted for 100% of the original carboxyl-reduced heparin, and paper chromatographic profiles of the oligosaccharide separations can be used as a fingerprint of the heparin preparation. The properties of I were examined in greater detail. The glycosidic bond of the L-idosyl 2-sulfate residue was found to be extremely labile to 0.1 N HCl at 100 degrees C, hydrolyzing with a t 1/2 of 18 min to give high yields of L-idose 2-sulfate and anhydro-D-mannitol 6-sulfate. L-Idofuranose was also identified as an intermediate in the conversion of L-idose 2-sulfate to L-idosan. The acid lability of the L-idosyl 2-sulfate bond in I offers a new route for the selective cleavage of carboxyl-reduced heparin.
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data (2012)

http://bioinformatics.mdanderson.org/main/BreakFusion
Zara Returns: Improved Personality Induction and Adaptation by an Empathetic Virtual Agent (2017)

Virtual agents need to adapt their personality to the user in order to become more empathetic. To this end, we developed Zara the Supergirl, an interactive empathetic agent, using a modular approach. In this paper, we describe the enhanced personality module with improved recognition from speech and text using deep learning frameworks. From raw audio, an average F-score of 69.6 was obtained from realtime personality assessment using a Convolutional Neural Network (CNN) model. From text, we improved personality recognition results with a CNN model on top of pre-trained word embeddings and obtained an average F-score of 71.0. Results from our Human-Agent Interaction study confirmed our assumption that people have different agent personality preferences. We use insights from this study to adapt our agent to user personality.
Synthesis of 5<i>H</i>‐pyrazolo[5,1‐<i>c</i>][1,4]benzodiazepine (1983)

Abstract The reaction of 2‐nitrobenzyl bromide with dimethyl pyrazole‐3, 5‐dicarboxylate gave dimethyl 1‐(2‐nitrobenzyl)pyrazole‐3, 5‐dicarboxylate which through a few steps procedure afforded the key intermediate 5, 10‐dihydro‐11‐oxopyrazolo[5, 1‐ c ][l, 4]benzodiazepine. The latter was reduced and dehydrogenated to yield the new tricyclic system 5 H ‐pyrazolo[5, 1‐ c ][1, 4]benzodiazepine.
The Discovery and Future Prospects of Artificial Porphyrins: Molecular Batteries Functioning with the Reversible Formation and Cleavage of Cyclopropane Units (1996)

The absence of the meso-hydrogen atoms in meso-octaalkylporphyrinogens enable the generation of novel forms of the oxidized porphyrinogen, 'artificial porphyrins'. A stepwise four-electron oxidation of meso-octaalkylporphyrinogen transitionmetal complexes led to an unusual aromatization of the porphyrinogen with the loss of four hydrogen atoms and the introduction of one, followed by two cyclopropane units into the porphyrinogen frame. Such oxidized forms of porphyrinogen function as two-electron shuttles via the formation and cleavage of the cyclopropane unit. Furthermore, the appropriate site opening of the cyclopropane may lead to important modifications of the porphyrinogen frame.
Nucleotide sequence and genome organization of Cucumber yellows virus, a member of the genus Crinivirus (2003)

The genome of Cucumber yellows virus (CuYV), isolated in Japan from cucumber (Cucumis sativus L.), was completely sequenced and shown to be bipartite. CuYV RNA1 consisted of 7889 nucleotides and encompassed seven open reading frames (ORFs), which is typical of the Closteroviridae, including a heat-shock protein 70 homologue, a coat protein and a diverged coat protein (CPd). CuYV RNA2 consisted of 7607 nucleotides and included two ORFs: ORF1a potentially encoded a polyprotein containing putative papain-like protease, methyltransferase and helicase domains, and ORF 1b potentially encoded an RNA-dependent RNA polymerase, which is probably expressed via a +1 ribosomal frameshift. The size and organization of the CuYV genome are similar to those of Lettuce infectious yellows virus (LIYV), the type member of the genus Crinivirus in the family Closteroviridae, indicating that CuYV is a member of that genus, although CuYV differed in several points from LIYV.
Towards Robust Animation of Complex Objects in Interaction (2006)

Le traitement robuste des collisions et des contacts est important dans les scénarios d'animation et de simulation par modèle physique. Un problème important est comment traiter les collisions et les auto-collisions simultanées se produisant entre les objets dans la scène. Nous présentons de nouvelles méthodes pour la simulation robuste des objets déformables complexes. Notre technique se base sur la détection continue et la détection discrète descollisions. Nous proposons deux approches pour traiter les collisions une fois qu'elles sont détectées. D'abord, nous modélisons les collisions comme des contraintes linéaires adjointes aux équations de la dynamique, ce qui aboutit à un problème de programmation quadratique (QP). À cet effet, nous avons développé un algorithme qui traite les équations dynamiques et les contraintes linéaires d'une manière globale. En second lieu, nous avons développé une méthode utilisant des pénalités qui traite les collisions multiples en exploitant la cohèrence temporelle. Le but est de garantir un état final sans collisions tout en réduisant au minimum la création des "collisions secondaires". Nous présentons nos résultats et analysons les avantages et la pertinence de notre méthode vis-à-vis des méthodes existantes. Les applications incluent les simulations mécaniques et chirurgicales, ainsi que les jeux vidéo et les effets spéciaux pour le cinéma
Investigation of thermal and electrical conductivity of graphene based nanofluids (2010)

We report for the first time, the synthesis of highly stable exfoliated graphene based nanofluids with water and ethylene glycol as base fluids with out any surfactant and the subsequent studies on their thermal and electrical conductivities. Graphene was synthesized by thermal exfoliation of graphene oxide at 1050 °C in Ar atmosphere. The as-synthesized graphene has been suitably functionalized and further dispersed it in the base fluids without any surfactant. Thermal and electrical conductivities of these nanofluids were measured for varying volume fractions and at different temperatures. An enhancement in thermal conductivity by about 14% has been achieved at 25 °C with deionized water (DI) as base fluid at a very low volume fraction of 0.056% which increases to about 64% at 50 °C. Electrical conductivity measurements for these nanofluids indicate an enormous enhancement at 25 °C for a volume fraction of 0.03%in DI water.
Low GSK-3β Immunoreactivity in Postmortem Frontal Cortex of Schizophrenic Patients (2000)

These results are consistent with the notion that schizophrenia involves neurodevelopmental pathology. It remains to be investigated whether the active fraction of GSK-3beta, or its activity, is also low in frontal cortex of schizophrenic patients and if this is also reflected in other brain regions.
BGPStream (2016)

We present BGPStream, an open-source software framework for the analysis of both historical and real-time Border Gateway Protocol (BGP) measurement data. Although BGP is a crucial operational component of the Internet infrastructure, and is the subject of research in the areas of Internet performance, security, topology, protocols, economics, etc., there is no efficient way of processing large amounts of distributed and/or live BGP measurement data. BGPStream fills this gap, enabling efficient investigation of events, rapid prototyping, and building complex tools and large-scale monitoring applications (e.g., detection of connectivity disruptions or BGP hijacking attacks). We discuss the goals and architecture of BGPStream. We apply the components of the framework to different scenarios, and we describe the development and deployment of complex services for global Internet monitoring that we built on top of it.
The application of high-order differencing to the scalar wave equation (1986)

Abstract The second-order central difference is often used to approximate the derivatives of the wave equation. It is demonstrated that gains in computational efficiency can be made by using high-order approximations for these derivatives. A one-dimensional model is used to illustrate the relative accuracy of O(Delta t 2 , Delta x 2 ), O(Delta t 2 , Delta x 4 ), O(Delta t 4 , Delta x 4 ), and O(Delta t 4 , Delta x 10 ) central-difference schemes. For comparison, O(Delta t 2 ) and O(Delta t 4 ) pseudo-spectral schemes are used as an additional measure of performance. The results indicate that O(Delta t 4 , Delta x 10 ) differencing can achieve similar accuracy as the O(Delta t 4 ) spectral scheme. For practical illustration, a two-dimensional form of the O(Delta t 4 , Delta x 10 ) algorithm is used to compute the exploding reflector response of a salt-dome model and compared with a fine-grid O(Delta t 2 , Delta x 4 ) result. Transmissive sponge-like boundary conditions are also examined and shown to be effective.
Handover in the 3GPP long term evolution (LTE) systems (2010)

One of the main goals of E-UTRAN is to provide seamless access to voice and multimedia services with strict delay requirements, which is achieved by supporting handover from source cell to target cell. Proper handover algorithms can make the system increased capacity, better coverage, higher throughput, reduced latency requirements. In this paper we give an overview of the LTE intra-access handover procedure, the simulation approach, and several latest handover algorithms which can enhance performance of the LTE systems are introduced. Finally the results show that the handover in the LTE system is complicated and imperfect, proper handover algorithms in the LTE system should be researched as quickly as possible.
Energy Management Optimization in a Battery/Supercapacitor Hybrid Energy Storage System (2011)

Batteries and supercapacitors (SC) complement one another; a battery has a relatively high energy density but a low power density, whereas an SC has a relatively high power density but a low energy density. In order to offset their opposing limitations, an active battery/SC hybrid energy storage system (HESS) using a dc/dc converter has been proposed. The major problem concerning an active HESS is in how to control the current flow in order to achieve two objectives: the minimization of the magnitude/fluctuation of the current flowing in and out of the battery and the energy loss seen by the SCs. This problem has not been analytically investigated for an optimal solution regarding these two goals. In this paper, we present an optimal energy management scheme for active HESS. In order to obtain the optimal solution, we formulate the problem as an optimization problem concerning these two objectives. Observing that the feasibility and optimality of the solution critically depends on the boundary parameters of the problem, we present an algorithm that effectively adjusts the parameter values. The proposed algorithm is based on the multiplicative-increase- additive-decrease principle, which guarantees a feasible optimal solution. Through MATLAB simulations, we demonstrate that the proposed scheme can optimally minimize the magnitude/fluctuation of the battery current and the SC energy loss.
Error detection by duplicated instructions in super-scalar processors (2002)

This paper proposes a pure software technique "error detection by duplicated instructions" (EDDI), for detecting errors during usual system operation. Compared to other error-detection techniques that use hardware redundancy, EDDI does not require any hardware modifications to add error detection capability to the original system. EDDI duplicates instructions during compilation and uses different registers and variables for the new instructions. Especially for the fault in the code segment of memory, formulas are derived to estimate the error-detection coverage of EDDI using probabilistic methods. These formulas use statistics of the program, which are collected during compilation. EDDI was applied to eight benchmark programs and the error-detection coverage was estimated. Then, the estimates were verified by simulation, in which a fault injector forced a bit-flip in the code segment of executable machine codes. The simulation results validated the estimated fault coverage and show that approximately 1.5% of injected faults produced incorrect results in eight benchmark programs with EDDI, while on average, 20% of injected faults produced undetected incorrect results in the programs without EDDI. Based on the theoretical estimates and actual fault-injection experiments, EDDI can provide over 98% fault-coverage without any extra hardware for error detection. This pure software technique is especially useful when designers cannot change the hardware, but they need dependability in the computer system. To reduce the performance overhead, EDDI schedules the instructions that are added for detecting errors such that "instruction-level parallelism" (ILP) is maximized. Performance overhead can be reduced by increasing ILP within a single super-scalar processor. The execution time overhead in a 4-way super-scalar processor is less than the execution time overhead in the processors that can issue two instructions in one cycle.
An intelligent search method for query optimization by semijoins (1989)

The problem of finding an optimal semijoin sequence that fully reduces a given tree query is discussed. A method is presented that intelligently navigates the space of all semijoin sequences and returns an optimal solution. Experiments are reported that show that this method performs very efficiently: on average, less than 5% of the search space is searched before an optimal solution is found. Other advantages of the method are ease of implementation, generality of the cost mode considered, and ability to handle tree queries with arbitrary target lists.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Idiopathic bile acid malabsorption--a review of clinical presentation, diagnosis, and response to treatment. (1991)

Between 1982 and 1989, the seven day retention of 75SeHCAT was measured in 181 patients with chronic diarrhoea that remained unexplained after full investigation. Altogether 121 of the 181 had a seven day 75SeHCAT retention greater than or equal to 15% and thus had no evidence of abnormal bile acid turnover. Twenty one had a seven day 75SeHCAT retention greater than or equal to 10% but less than 15%. Their clinical features were typical of the irritable bowel syndrome, and none of eight treated with cholestyramine showed symptomatic improvement. Sixteen patients had a seven day retention greater than or equal to 5% and less than 10%, six of whom had improved symptoms after treatment with bile acid chelating agents. The remaining 23 patients had a 75SeHCAT retention of less than 5% at seven days and responded to bile acid chelators. This group had a characteristic illness with intermittent watery diarrhoea, but no constitutional upset. It was not possible to distinguish the patients with bile acid malabsorption exclusively on the basis of the clinical symptoms and investigations, other than 75SeHCAT retention. We conclude that the measurement of 75SeHCAT retention is useful, appropriate, and necessary in patients with unexplained chronic diarrhoea.
Static power supplies for adjustable-speed drives (1962)

Static power supplies are being used increasingly to provide adjustable speeds for industrial applications. Among the advantages are elimination of rotating equipment, low maintenance, high efficiency, flexibility, compactness, and adaptability to automation
Cellulose crystallinity index: measurement techniques and their impact on interpreting cellulase performance (2010)

Although measurements of crystallinity index (CI) have a long history, it has been found that CI varies significantly depending on the choice of measurement method. In this study, four different techniques incorporating X-ray diffraction and solid-state 13C nuclear magnetic resonance (NMR) were compared using eight different cellulose preparations. We found that the simplest method, which is also the most widely used, and which involves measurement of just two heights in the X-ray diffractogram, produced significantly higher crystallinity values than did the other methods. Data in the literature for the cellulose preparation used (Avicel PH-101) support this observation. We believe that the alternative X-ray diffraction (XRD) and NMR methods presented here, which consider the contributions from amorphous and crystalline cellulose to the entire XRD and NMR spectra, provide a more accurate measure of the crystallinity of cellulose. Although celluloses having a high amorphous content are usually more easily digested by enzymes, it is unclear, based on studies published in the literature, whether CI actually provides a clear indication of the digestibility of a cellulose sample. Cellulose accessibility should be affected by crystallinity, but is also likely to be affected by several other parameters, such as lignin/hemicellulose contents and distribution, porosity, and particle size. Given the methodological dependency of cellulose CI values and the complex nature of cellulase interactions with amorphous and crystalline celluloses, we caution against trying to correlate relatively small changes in CI with changes in cellulose digestibility. In addition, the prediction of cellulase performance based on low levels of cellulose conversion may not include sufficient digestion of the crystalline component to be meaningful.
Women, Wages and Industrial Relations in Australia: The Past, the Present and the Future (2006)

Between 2000 and 2002 state industrial tribunals in New South Wales and Queensland adopted new equal remuneration principles and recast institutional approaches to the valuation of feminised work. These principles advanced the concept of gender pay equity and addressed something of a policy hiatus that followed the breakthrough provided by the 1972 equal pay for equal work doctrine. The new principles have been utilised to obtain significant award wage increases for undervalued areas of feminised work. Yet their influence will be a short-lived one due to the Howard government's Work Choices legislation. New federal laws specifically exclude the operation of the state equal remuneration principles and do not provide any substitute agency or process in their place. Coupled with a policy agenda that enshrines individual and enterprise agreements, these laws mean that gender pay equity can no longer be addressed on a collective basis in Australia.
Fibronectin-, vitronectin- and laminin-binding proteins at the cell walls of Candida parapsilosis and Candida tropicalis pathogenic yeasts (2015)

Our results reveal new insight into host-pathogen interactions during infections by two important, recently emerging, fungal pathogens.
Thermotropic phase behavior of model membranes composed of phosphatidylcholines containing methyl iso-branched fatty acids. 1. Differential scanning calorimetric studies (1985)

The thermotropic phase behavior of aqueous dispersions of phosphatidylcholines containing one of a series of methyl iso-branched fatty acyl chains was studied by differential scanning calorimetry. These compounds exhibit a complex phase behavior on heating which includes two endothermic events, a gel/gel transition, involving a molecular packing rearrangement between two gel-state forms, and a gel/liquid-crystalline phase transition, involving the melting of the hydrocarbon chains. The gel to liquid-crystalline transition is a relatively fast, highly cooperative process which exhibits a lower transition temperature and enthalpy than do the chain-melting transitions of saturated straight-chain phosphatidylcholines of similar acyl chain length. In addition, the gel to liquid-crystalline phase transition temperature is relatively insensitive to the composition of the aqueous phase. In contrast, the gel/gel transition is a slow process of lower cooperativity than the gel/liquid-crystalline phase transition and is sensitive to the composition of the bulk aqueous phase. The gel/gel transitions of the methyl iso-branched phosphatidylcholines have very different thermodynamic properties and depend in a different way on hydrocarbon chain length than do either the "subtransitions" or the "pretransitions" observed with linear saturated phosphatidylcholines. The gel/gel and gel/liquid-crystalline transitions are apparently concomitant for the shorter chain iso-branched phosphatidylcholines but diverge on the temperature scale with increasing chain length, with a pronounced odd/even alternation of the characteristic temperatures of the gel/gel transition.(ABSTRACT TRUNCATED AT 250 WORDS)
Visibility-Graph-Based Shortest-Path Geographic Routing in Sensor Networks (2009)

We study the problem of shortest-path geographic routing in a static sensor network. Existing algorithms often make routing decisions based on node information in local neighborhoods. However, it is shown by Kuhn et al. that such a design constraint results in a highly undesirable lower bound for routing performance: if a best route has length c, then in the worst case a route produced by any localized algorithm has length Omega(c <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), which can be arbitrarily worse than the optimal. We present VIGOR, a visibility-graph-based routing protocol that produces routes of length Theta(c). Our design is based on the construction of a much reduced visibility graph, which guides nodes to find near-optimal paths. The per-node protocol overheads in terms of state information and message transmission depend only on the complexity of the field's large topological features, rather than on the network size. Simulation results show that our protocol dramatically outperforms localized protocols such as GPSR and GOAFR+ in both average and worst cases, with reasonable extra overheads.