gebhart/patrepeval huggingface dataset:
Fast sparse matrix multiplication (2005)

Let A and B two n × n matrices over a ring R (e.g., the reals or the integers) each containing at most m nonzero elements. We present a new algorithm that multiplies A and B using O ( m 0.7 n 1.2 + n 2+ o (1) ) algebraic operations (i.e., multiplications, additions and subtractions) over R . The naïve matrix multiplication algorithm, on the other hand, may need to perform Ω( mn ) operations to accomplish the same task. For m ≤ n 1.14 , the new algorithm performs an almost optimal number of only n 2+ o (1) operations. For m ≤ n 1.68 , the new algorithm is also faster than the best known matrix multiplication algorithm for dense matrices which uses O ( n 2.38 ) algebraic operations. The new algorithm is obtained using a surprisingly straightforward combination of a simple combinatorial idea and existing fast rectangular matrix multiplication algorithms. We also obtain improved algorithms for the multiplication of more than two sparse matrices. As the known fast rectangular matrix multiplication algorithms are far from being practical, our result, at least for now, is only of theoretical value.
Immunologic memory to phosphorylcholine. VI. Heterogeneity in light chain gene expression (1985)

BALB/c mice immunized with phosphorylcholine-conjugated keyhole limpet hemocyanin (PC-KLH) produce two types of anti-PC antibodies, designated group I and group II, which differ in their fine specificity and idiotype expression. Group II hybridomas can utilize VH genes and VL genes (in particular, V kappa 1-3) distinct from those expressed in the group I-like anti-PC myelomas. Here we have analyzed additional anti-PC hybridomas from BALB/c and (CBA/N X BALB/c)F1 male mice and also anti-PC antibodies purified from BALB/c and C57BL/6N antisera. Isoelectric focusing indicates that one of the group II hybridomas utilizes V kappa 1-3 and that related L chains are expressed in a major portion of group II serum antibodies. Other group II antibodies in antisera express different L chains, some of which are presently unidentified. However, isoelectric focusing analysis also indicates that the L chains of some group II hybridomas and serum antibodies are related to those found in the group I anti-PC myelomas and group I hybridoma and serum antibodies. In addition, one hybridoma was found to utilize lambda 2. Thus, it appears that the anti-PC antibodies with group II-like fine specificity can utilize a variety of VL genes related to, or distinct from, those expressed in group I antibodies.
Exciton Spin Currents: Theory (2013)

An indirect exciton is a bound pair of an electron and a hole confined in spatially separated semiconductor layers. Long lifetimes of indirect excitons allow them to cool down to low temperatures below the temperature of quantum degeneracy. In coherent exciton gases the spin relaxation mechanisms linked with the scattering of particles are strongly suppressed. Recent experiments evidenced spontaneous coherence and condensation, phase singularities, spatial ordering, and polarization textures in a cold excitons gas . We develop a theoretical model accounting for the spin-orbit interaction of electrons and holes, exchange splitting of exciton states and Zeeman effect. This model describes the polarization patterns observed experimentally, including helical patterns, four-leaf patterns, spiral patterns, and bell patterns, and confirms that the polarization textures at low temperature manifest ballistic propagation of cold excitons over the distances exceeding the exciton Bohr radius by 3 orders of magnitude and the exciton thermal De Broglie wavelength by more than an order of magnitude. The comparison of theory and experiment allows extracting the spin currents carried by electrons and holes bound to excitons. The spins tend to align along the effective spin-orbit field induced due to the Dresselhaus effect.
Activation of selenate by adenosine 5′-triphosphate sulphurylase from Saccharomyces cerevisiae (1977)

In the presence of ATP and Mg2+, ATP sulphurylase from Saccharomyces cerevisiae catalysed the conversion of selenate into a compound with the electrophoretic and acid-lability properties of adenosine 5'-sulphatophosphate. Structural characterization, involving extensive purification of adenosine 5'-selenophosphate, proved impossible. However, we showed ATP-, Mg2+- and ATP sulphurylase-dependent, and inorganic pyrophosphatase-stimulated, production of elemental selenium from selenate in the presence of GSH (reduced glutathione). Since selenate was not reduced by GSH, this reaction proved that ATP sulphurylase had formed an active selenate. The enzyme catalysed formation of elemental selenium had the same kinetics and GSH-dependency as the non-enzymic reduction of selenite to elemental selenium by GSH. In the presence of inorganic pyrophosphatase, 2 mol of Pi was released for each mol of 'active selenate' formed. This was shown by a spectrophotometric assay for elemental selenium. The observed reactivity with thiols and the instability of the enzymic product were those predicted for selenium anhydrides. By analogy with the chemistry of sulphur, the product of the thiolytic cleavage of a selenium anhydride would be converted into selenite. The selenite would then be reduced by the thiol to elemental selenium. We conclude that ATP sulphurylase can catalyse the formation of adenosine 5'-selenophosphate. The anhydride can be reduced by thiols in a manner similar to the reduction of selenite. These results probably explain the ability of mammals, lacking a sulphate reductase system, to incorporate selenium from selenate into seleno-amino acids.
Creation of the Probationary Division of Chemical Toxicology (1996)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTCreation of the Probationary Division of Chemical ToxicologyLawrence J. MarnettView Author Information Editor Cite this: Chem. Res. Toxicol. 1996, 9, 1, 1–2Publication Date (Web):January 15, 1996Publication History Published online15 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/tx9504624https://doi.org/10.1021/tx9504624editorialACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views385Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (38 KB) Get e-AlertscloseSUBJECTS:Genetics,Testing and assessment,Toxicity,Toxicology Get e-Alerts
OWL Web Ontology Language XML Presentation Syntax (2003)

hori2003a
AtRH57, a DEAD‐box RNA helicase, is involved in feedback inhibition of glucose‐mediated abscisic acid accumulation during seedling development and additively affects pre‐ribosomal RNA processing with high glucose (2013)

The Arabidopsis thaliana T-DNA insertion mutant rh57-1 exhibited hypersensitivity to glucose (Glc) and abscisic acid (ABA). The other two rh57 mutants also showed Glc hypersensitivity similar to rh57-1, strongly suggesting that the Glc-hypersensitive feature of these mutants results from mutation of AtRH57. rh57-1 and rh57-3 displayed severely impaired seedling growth when grown in Glc concentrations higher than 3%. The gene, AtRH57 (At3g09720), was expressed in all Arabidopsis organs and its transcript was significantly induced by ABA, high Glc and salt. The new AtRH57 belongs to class II DEAD-box RNA helicase gene family. Transient expression of AtRH57-EGFP (enhanced green fluorescent protein) in onion cells indicated that AtRH57 was localized in the nucleus and nucleolus. Purified AtRH57-His protein was shown to unwind double-stranded RNA independent of ATP in vitro. The ABA biosynthesis inhibitor fluridone profoundly redeemed seedling growth arrest mediated by sugar. rh57-1 showed increased ABA levels when exposed to high Glc. Quantitative real time polymerase chain reaction analysis showed that AtRH57 acts in a signaling network downstream of HXK1. A feedback inhibition of ABA accumulation mediated by AtRH57 exists within the sugar-mediated ABA signaling. AtRH57 mutation and high Glc conditions additively caused a severe defect in small ribosomal subunit formation. The accumulation of abnormal pre-rRNA and resistance to protein synthesis-related antibiotics were observed in rh57 mutants and in the wild-type Col-0 under high Glc conditions. These results suggested that AtRH57 plays an important role in rRNA biogenesis in Arabidopsis and participates in response to sugar involving Glc- and ABA signaling during germination and seedling growth.
Negative Results for Software Effort Estimation (2016)

Context:More than half the literature on software effort estimation (SEE) focuses on comparisons of new estimation methods. Surprisingly, there are no studies comparing state of the art latest methods with decades-old approaches. Objective:To check if new SEE methods generated better estimates than older methods. Method: Firstly, collect effort estimation methods ranging from "classical" COCOMO (parametric estimation over a pre-determined set of attributes) to "modern" (reasoning via analogy using spectral-based clustering plus instance and feature selection, and a recent "baseline method" proposed in ACM Transactions on Software Engineering).Secondly, catalog the list of objections that lead to the development of post-COCOMO estimation methods.Thirdly, characterize each of those objections as a comparison between newer and older estimation methods.Fourthly, using four COCOMO-style data sets (from 1991, 2000, 2005, 2010) and run those comparisons experiments.Fifthly, compare the performance of the different estimators using a Scott-Knott procedure using (i) the A12 effect size to rule out "small" differences and (ii) a 99% confident bootstrap procedure to check for statistically different groupings of treatments). Results: The major negative results of this paper are that for the COCOMO data sets, nothing we studied did any better than Boehm's original procedure. Conclusions: When COCOMO-style attributes are available, we strongly recommend (i) using that data and (ii) use COCOMO to generate predictions. We say this since the experiments of this paper show that, at least for effort estimation,how data is collected is more important than what learner is applied to that data.
SEVERE PENETRATING EYE TRAUMA CAUSED BY FISH PICK ACCIDENTS (1996)

These injuries differ from fish hook injuries because the instrument is much larger and is blunt in nature, imparting significant energy into the eye. Consequently, patients with these injuries have a much less favorable outcome.
Harmony: Towards Automated Self-Adaptive Consistency in Cloud Storage (2012)

In just a few years cloud computing has become a very popular paradigm and a business success story, with storage being one of the key features. To achieve high data availability, cloud storage services rely on replication. In this context, one major challenge is data consistency. In contrast to traditional approaches that are mostly based on strong consistency, many cloud storage services opt for weaker consistency models in order to achieve better availability and performance. This comes at the cost of a high probability of stale data being read, as the replicas involved in the reads may not always have the most recent write. In this paper, we propose a novel approach, named Harmony, which adaptively tunes the consistency level at run-time according to the application requirements. The key idea behind Harmony is an intelligent estimation model of stale reads, allowing to elastically scale up or down the number of replicas involved in read operations to maintain a low (possibly zero) tolerable fraction of stale reads. As a result, Harmony can meet the desired consistency of the applications while achieving good performance. We have implemented Harmony and performed extensive evaluations with the Cassandra cloud storage on Grid'5000 test bed and on Amazon EC2. The results show that Harmony can achieve good performance without exceeding the tolerated number of stale reads. For instance, in contrast to the static eventual consistency used in Cassandra, Harmony reduces the stale data being read by almost 80% while adding only minimal latency. Meanwhile, it improves the throughput of the system by 45% while maintaining the desired consistency requirements of the applications when compared to the strong consistency model in Cassandra.
Generalized Terrain Topography in Radar Scattering Models (2016)

Modeling of terrain topography is crucial for vegetated areas given that even small slopes impact and alter the radar wave interactions between the ground and the overlying vegetation. Current missions either exclude pixels with large topographic slopes or disregard the terrain topography entirely, potentially accumulating substantial modeling errors and therefore impacting the retrieval performance over such sloped pixels. The underlying terrain topography needs to be considered and modeled to obtain a truly general and accurate radar scattering model. In this paper, a flexible and modular model is developed: the vegetation is considered by a multilayered multispecies vegetation model capable of representing a wide range of vegetation cover types ranging from bare soil to dense forests. The ground is incorporated with the stabilized extended boundary condition method, allowing the representation of an N-layered soil structure with rough interfaces. Terrain topography is characterized by a 2-D slope with two tilt angles (α, β). Simulation results for an evergreen forest show the impact of a 2-D slope for a range of tilt angles: a 10° tilt in the plane of incidence translates to a change of up to 15 dB in 1111, 10 dB in VV, and 1.5 dB in 11V for the total radar backscatter. Terrain topography is shown to be crucial for accurate forward modeling, especially over forested areas.
Infrared continuum radiation from high and ultra-high pressure mercury lamps (2005)

Infrared (IR) continuum radiation from the arc of high and ultra-high pressure (UHP) mercury lamps was measured and modelled. Three major contributions to the IR continuum are electron–atom bremsstrahlung, which is dominant, electron–ion bremsstrahlung and electron–ion recombination radiation. The line width of the resonance broadened Hg 71S0 to 61P1 transition at 1014 nm was used to determine the arc core Hg density, and the radiance of this line was used to determine the arc temperature as a function of radius. The temperature map for the UHP lamp was checked using the Bartels method on the 546 nm line of Hg. Model results based on recently published electron–atom bremsstrahlung coefficients were found to be in good agreement with measurements across the near IR.
A Computational Model for Simulating Proppant Transport in Wellbore and Fractures for Unconventional Treatments (2014)

Abstract This paper presents a new and comprehensive model for proppant transport that is applicable inside both the wellbore and the fracture, along with an appropriate fast computational algorithm. This model can be used efficiently in both real-time and design modes of hydraulic fracturing processes. The spatio-temporal proppant evolution is crucial in hydraulic fracturing processes as it directly affects production during shut-in and flowback. Yet, the computational cost is quite high because of multidimensional multiphase flow models, while most of the numerical approximations, such as the standard Galerkin finite element, are limited in their validity, prohibiting the numerical models from properly modeling the proppant dynamics correctly and practically. This paper discusses a new one-dimensional (1D) two-phase flow model that accounts for the leading two-dimensional (2D) effects, such as proppant settling, resuspension, and bed transport, among others. Accounting for these effects helps ensure the conservation of momentum and mass conservation for the fluid flow for the proppant as well as for the proppant bed transport. The momentum conservation equations embed the interphase momentum transfer between the fluid and the solid phases, the momentum changes caused by proppant settling and resuspension, and the momentum exchange associated with the shear on the dynamic built-up proppant bed. This is accompanied by the mass conservations equations to include the fluid and the proppant mass flux induced by the settling and resuspension. This computational model simulates proppant transport by using a first-order implicit scheme in time and first-order upwind scheme in space for the convection over a collocated grid for flow variables. The simulations demonstrate that the proppant bed is gradually formed and expanded downstream. These simulations also show that the formation of the proppant bed is caused mainly by proppant settling, and height change is determined by interactions among proppant settling and its resuspension during transport. Also, it is shown that the proppant properties strongly affect slurry transport and proppant bed dynamics. The general results provide insight into the different mechanisms of the transport process, including gravitational settling and resuspension of proppant and proppant bed buildup and transport inside both the wellbore and fractures. This model provides a more pragmatic approach that enables field engineers to gain better insight into the proppant transport phenomena during a fracturing treatment.
On the impact of control channel reliability on coordinated multi-point transmission (2014)

In the heterogeneous networks (HetNets), co-channel interference is a serious problem. Coordinated multi-point (CoMP) transmission has emerged as a powerful technique to mitigate co-channel interference. However, all CoMP techniques rely on information exchange through reliable control channels, which are unlikely to be available in HetNets. In this paper, we study the effect of unreliable control channels, consisting of the access links and backhaul links, on the performance of CoMP. A control channel model is introduced by assigning link failure probability (LFP) to backhaul and access links for the cooperative clusters. Three CoMP architectures, namely the centralized, semi-distributed, and fully distributed are analyzed. We investigate the probability of deficient control channels reducing quality of service and impeding transmission. General closed form expressions are derived for the probability of a cooperative transmission node staying silent in a resource slot due to unreliable control links. By evaluating the average sum rate of users within a CoMP cluster, we show that the performance gains offered by CoMP quickly diminish, as the unreliability of the control links grows.
Reactive Supervisory Control of Open Discrete Event Systems (2019)

The conventional Wonham-Ramadge supervisory control framework of discrete event systems enforces a closed discrete event system to generate correct behaviors under certain environments, which can be captured by an appropriate plant model. Nevertheless, such control methods cannot be directly applied for many practical engineering systems nowadays since they are open systems and their operation heavily depends on nontrivial interactions between the systems and the external environments. These open systems should be controlled in such a way that accomplishment of the control objective can be guaranteed for any possible environment, which may be dynamic, uncertain and sometimes unpredictable. In this paper, we aim at extending the conventional supervisory control theory to open discrete event systems in a reactive manner. Starting from a novel input-output automaton model of an open system, we consider control objectives that characterize the desired input-output behaviors of the system, based on which a game-theoretic approach is carried out to compute a reactive supervisor that steers the system to fulfill the specifications regardless of the environment behaviors. We present a necessary and sufficient conditions for the existence of such a reactive supervisor. Furthermore, illustrative examples are given throughout this paper to demonstrate the key definitions and the effectiveness of the proposed reactive supervisor synthesis framework.
How biochar works, and when it doesn't: A review of mechanisms controlling soil and plant responses to biochar (2021)

Abstract We synthesized 20 years of research to explain the interrelated processes that determine soil and plant responses to biochar. The properties of biochar and its effects within agricultural ecosystems largely depend on feedstock and pyrolysis conditions. We describe three stages of reactions of biochar in soil: dissolution (1–3 weeks); reactive surface development (1–6 months); and aging (beyond 6 months). As biochar ages, it is incorporated into soil aggregates, protecting the biochar carbon and promoting the stabilization of rhizodeposits and microbial products. Biochar carbon persists in soil for hundreds to thousands of years. By increasing pH, porosity, and water availability, biochars can create favorable conditions for root development and microbial functions. Biochars can catalyze biotic and abiotic reactions, particularly in the rhizosphere, that increase nutrient supply and uptake by plants, reduce phytotoxins, stimulate plant development, and increase resilience to disease and environmental stressors. Meta‐analyses found that, on average, biochars increase P availability by a factor of 4.6; decrease plant tissue concentration of heavy metals by 17%–39%; build soil organic carbon through negative priming by 3.8% (range −21% to +20%); and reduce non‐CO 2 greenhouse gas emissions from soil by 12%–50%. Meta‐analyses show average crop yield increases of 10%–42% with biochar addition, with greatest increases in low‐nutrient P‐sorbing acidic soils (common in the tropics), and in sandy soils in drylands due to increase in nutrient retention and water holding capacity. Studies report a wide range of plant responses to biochars due to the diversity of biochars and contexts in which biochars have been applied. Crop yields increase strongly if site‐specific soil constraints and nutrient and water limitations are mitigated by appropriate biochar formulations. Biochars can be tailored to address site constraints through feedstock selection, by modifying pyrolysis conditions, through pre‐ or post‐production treatments, or co‐application with organic or mineral fertilizers. We demonstrate how, when used wisely, biochar mitigates climate change and supports food security and the circular economy.
Formation of Giant Needle‐Like Polycation‐Bile Acid Complexes (2003)

Abstract The complexation of bile acids with various solvated polycations was studied. A one‐to‐one complex was precipitated when an aqueous solution of cholic acid sodium salt (CA) was mixed with aqueous solutions of 3,3‐ionene and grew to form crystals with needle‐like morphology, 3 millimeters in length. Hydrogen bonding of hydroxyls at the steroid face and the spacing between cationic sites of polycations were crucial for the formation of the giant needle. Crossed polarizing microscopic photograph of the complex composed of cholic acid sodium salt and 3,3‐ionene. magnified image Crossed polarizing microscopic photograph of the complex composed of cholic acid sodium salt and 3,3‐ionene.