gebhart/patrepeval huggingface dataset:
Identifying Extract Method Refactoring Opportunities Based on Functional Relevance (2016)

`Extract Method' is considered one of the most frequently applied and beneficial refactorings, since the corresponding Long Method smell is among the most common and persistent ones. Although Long Method is conceptually related to the implementation of diverse functionalities within a method, until now, this relationship has not been utilized while identifying refactoring opportunities. In this paper we introduce an approach (accompanied by a tool) that aims at identifying source code chunks that collaborate to provide a specific functionality, and propose their extraction as separate methods. The accuracy of the proposed approach has been empirically validated both in an industrial and an open-source setting. In the former case, the approach was capable of identifying functionally related statements within two industrial long methods (approx. 500 LoC each), with a recall rate of 93 percent. In the latter case, based on a comparative study on open-source data, our approach ranks better compared to two well-known techniques of the literature. To assist software engineers in the prioritization of the suggested refactoring opportunities the approach ranks them based on an estimate of their fitness for extraction. The provided ranking has been validated in both settings and proved to be strongly correlated with experts' opinion.
Effects of edge inclination angles on whispering-gallery modes in printable wedge microdisk lasers (2018)

The ink-jet technique was developed to print the wedge polymer microdisk lasers. The characterization of these lasers was implemented using a free-space optics measurement setup. It was found that disks of larger edge inclination angles have a larger free spectral range (FSR) and a lower resonance wavelength difference between the fundamental transverse electric (TE) and transverse magnetic (TM) whispering-gallery modes (WGMs). This behavior was also confirmed with simulations based on the modified Oxborrow's model with perfectly matched layers (PMLs), which was adopted to accurately calculate the eigenfrequencies, electric field distributions, and quality parameters of modes in the axisymmetric microdisk resonators. Combined with the nearly equivalent quality factor (Q-factor) and finesse factor (F-factor) variations, the correlations between the TE and left adjacent TM modes were theoretically demonstrated. When the edge inclination angle is varied, the distinguishable mode distribution facilitates the precise estimation of a resonance wavelength shift. Therefore, the flexible and efficient nature of wedge polymer microdisk lasers extends their potential applications in precision sensing technology.
Intracuff Pressure and Tracheal Morbidity (2001)

Excess in endotracheal tube cuff pressure during balanced anesthesia due to nitrous oxide diffusion into this closed gas space causes sore throat that is related to tracheal mucosal erosion.
Finger Flexors Fatigue in Trained Rock Climbers and Untrained Sedentary Subjects (2003)

The present series of experiments were conducted to access the surface EMG frequency parameters during repeated fingertip isometric contractions to determine if they can be used as a fatigue index under specific grip used in rock climbing. Electromyograms of the finger flexors and extensors were characterised in ten elite climbers and ten non-climbers. The exercise consisted in reaching 80 % of maximal isometric finger force as quickly as possible intermittently with a 5-s contraction followed by 5-s of rest until exhaustion (i. e. when the subject was unable to maintain 80 - 70 % MVC force range for the 5 s). The results clearly indicate that expert climbers performed significantly greater fingertip force than sedentary subjects (420 +/- 46 N vs. 342 +/- 56 N). This force was maintained during twelve repetitions (12.88 +/- 4.96) in sedentary subjects, whereas the climbers maintained the force during nineteen repetitions (19.33 +/- 4.84). The median frequency of both the flexor and extensor EMG power spectra decreased during fatiguing isometric contractions, but at different rates in climbers and non-climbers. In non-climbers, the results replicated previous findings, whereas in climbers the results were novel.
Dynamic actin filaments control the mechanical behavior of the human red blood cell membrane (2015)

Short, uniform-length actin filaments function as structural nodes in the spectrin-actin membrane skeleton to optimize the biomechanical properties of red blood cells (RBCs). Despite the widespread assumption that RBC actin filaments are not dynamic (i.e., do not exchange subunits with G-actin in the cytosol), this assumption has never been rigorously tested. Here we show that a subpopulation of human RBC actin filaments is indeed dynamic, based on rhodamine-actin incorporation into filaments in resealed ghosts and fluorescence recovery after photobleaching (FRAP) analysis of actin filament mobility in intact RBCs (~25-30% of total filaments). Cytochalasin-D inhibition of barbed-end exchange reduces rhodamine-actin incorporation and partially attenuates FRAP recovery, indicating functional interaction between actin subunit turnover at the single-filament level and mobility at the membrane-skeleton level. Moreover, perturbation of RBC actin filament assembly/disassembly with latrunculin-A or jasplakinolide induces an approximately twofold increase or ~60% decrease, respectively, in soluble actin, resulting in altered membrane deformability, as determined by alterations in RBC transit time in a microfluidic channel assay, as well as by abnormalities in spontaneous membrane oscillations (flickering). These experiments identify a heretofore-unrecognized but functionally important subpopulation of RBC actin filaments, whose properties and architecture directly control the biomechanical properties of the RBC membrane.
An efficient reconstruction algorithm for differential phase-contrast tomographic images from a limited number of views (2015)

The main focus of this paper is reconstruction of tomographic phase-contrast image from a set of projections. We propose an efficient reconstruction algorithm for differential phase-contrast computed tomography that can considerably reduce the number of projections required for reconstruction. The key result underlying this research is a projection theorem that states that the second derivative of the projection set is linearly related to the Laplacian of the tomographic image. The proposed algorithm first reconstructs the Laplacian image of the phase-shift distribution from the second-derivative of the projections using total variation regularization. The second step is to obtain the phase-shift distribution by solving a Poisson equation whose source is the Laplacian image previously reconstructed under the Dirichlet condition. We demonstrate the efficacy of this algorithm using both synthetically generated simulation data and projection data acquired experimentally at a synchrotron. The experimental phase data were acquired from a human coronary artery specimen using dark-field-imaging optics pioneered by our group. Our results demonstrate that the proposed algorithm can reduce the number of projections to approximately 33% as compared with the conventional filtered backprojection method, without any detrimental effect on the image quality.
The Kinetics of the Chromate-Dichromate Reaction as Studied by a Relaxation Method (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Kinetics of the Chromate-Dichromate Reaction as Studied by a Relaxation MethodJames H. Swinehart and Gilbert W. CastellanCite this: Inorg. Chem. 1964, 3, 2, 278–280Publication Date (Print):February 1, 1964Publication History Published online1 May 2002Published inissue 1 February 1964https://pubs.acs.org/doi/10.1021/ic50012a033https://doi.org/10.1021/ic50012a033research-articleACS PublicationsRequest reuse permissionsArticle Views458Altmetric-Citations20LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Estimation of the degree of crystallographic ordering of magnetoactive ions in Sr2FeMoO6-δ by means of the intensity of the X-ray peak (101) (2019)

Strontium ferromolybdate (Sr 2 FeMoO 6-δ , SFMO) having a double Perovskite structure shows good promise as a basic material for spintronics. However SFMO has not yet found wide application due to the low reproducibility of its magnetic properties which partially originates from their strong dependence on the ordering degree of Fe and Mo ions in the B ´ and B ² sublattices of double perovskite A 2 B ´ B ²O 6 . We have considered a rapid method of determining strontium ferromolybdate disorder degree. Sublattice population with Fe and Mo ions has been estimated for stoichiometric and nonstoichiometric Sr 2 FeMoO 6- δ with a 5% Fe and Mo excess, respectively. We have calculated the intensity ratio between the superstructural ordering (101) peak and the most intense (112 + 200) peak. The calculated curves have been fitted to the analytical expression for similar cases known from literature. The calculation results obtained using this method are in agreement with the results of experimental data processing using the Rietveld method accurate to within ±25 %. Thus this method can be used instead of the Rietveld method if the exposure time set in an X-ray diffraction experiment is insufficient. We have discussed the dependence of the I (101)/ I (112 + 200) peak intensity ratio on various factors including diffraction peak instrumental broadening, peak twinning due to grain size reduction, thin film lattice parameter variation due to substrate lattice mismatch and lattice parameter variation due to oxygen vacancies. The method is useful as it allows evaluating the superlattice ordering degree in Sr 2 FeMoO 6- d without large time consumption for X-ray diffraction pattern recording and processing with the Rietveld method which may be essential when dealing with large amounts of experimental data
A Comparative Analysis of Blockchain Architecture and its Applications: Problems and Recommendations (2019)

In the past few years, the implementation of blockchain technology for various applications has been widely discussed in the research community and the industry. There are sufficient number of articles that discuss the possibility of applying blockchain technology in various areas, such as, healthcare, IoT, and business. However, in this article, we present a comparative analysis of core blockchain architecture, its fundamental concepts, and its applications in three major areas: the Internet-of-Things (IoT), healthcare, business and vehicular industry. For each area, we discuss in detail, challenges and solutions that have been proposed from the research community and industry. This research studies also presented the complete ecosystem of blockchain of all the papers we reviewed and summarized. Moreover, analysis is performed of various blockchain platforms, their consensus models, and applications. Finally, we discuss key aspects that are required for the widespread future adoption of blockchain technology in these major areas.
Experimentelle Untersuchungen über den Einfluß der Zwerchfellmotorik und des intraabdominellen Druckes auf die Leberdurchblutung (1970)

Durch Untersuchungen an narkotisierten Hunden wurde nachgewiesen, daß durch Ausschaltung der Zwerchfelltätigkeit und Änderung des intraabdominellen Druckes und der Atemmechanik die hepatale Zirkulation erheblich beeinflußt werden kann. Beim spontanatmenden Tier ist sowohl das arterielle als auch das portale Stromvolumen der Leber gegenüber den relaxierten und bilateral thorakotomierten Tieren gesteigert. Die Zunahme des Gesamt-Flow betrug durchschnittlich 37 ± ll,7%. Dabei summieren sich in unseren Versuchen drei wesentliche Effekte, die jeweils allein bereits eine Verbesserung der Leberdurchblutung zur Folge haben können:
<title>LLAB model for color appearance and color difference evaluation</title> (1996)

An ideal system of colorimetry should provide measures agreeing to what we see in three respects: color specification, difference and appearance. A successful method to quantify these measures depends upon the reliability of psychophysical experimental data. These data sets have been accumulated and were used to derive the LLAB model. The model includes two parts: a chromatic adaptation transform and a uniform color space. Tristimulus values under a particular set of illuminant/observer conditions are transformed to those of D65/2 degree(s) conditions via a chromatic adaptation transform. A modified version of CIELAB is then used to calculate six perceived attributes: lightness (L<SUB>L</SUB>), redness-greenness (A<SUB>L</SUB>), yellowness-blueness (B<SUB>L</SUB>), colorfulness (C<SUB>L</SUB>), hue angle (h<SUB>L</SUB>) and hue composition (H<SUB>L</SUB>). The model gives similar degree of prediction in comparison with the other state of the art models using the accumulated data sets. The LLAB model demonstrates that it is possible to achieve a system, which provides precise measures to quantify color match, difference and appearance.
Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets (2022)

Abstract Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWAS). Standard GWAS are well-powered to interrogate additive models; however, new approaches are required to investigate other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected due to lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWAS excludes detection of sites in LD that may underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta’s D statistics) in long-range LD (&gt; 0.25cM). We identified five significant associations across five disease phenotypes that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were 1) members of highly conserved gene families with complex roles in multiple pathways, 2) essential genes, and/or 3) associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and may especially be driving factors in conditions with a wide range of phenotypic outcomes. Significance Current knowledge of genotype-phenotype relationships is largely contingent on traditional univariate approaches to genomic analysis. Yet substantial evidence supports non-additive modes of inheritance and regulation, such as epistasis, as being abundant across the genome. In this genome-wide study, we probe the biomolecular mechanisms underlying complex human diseases by testing the association of pairwise genetic interactions with disease occurrence in large-scale biobank data. Specifically, we tested intrachromosomal and interchrosomal long-range interactions between regions of the genome in high linkage disequilibrium, these regions are typically excluded from genomic analyses. The results from this study suggest that essential gene, members of highly conserved gene families, and phenotypes with variable expressivity, are particularly enriched with epistatic and pleiotropic activity.
Fibrinolysis. I. Fibrinolytic Activity of Extracts from non-Pathogenic fungi. (1958)

A study of properties of extracts from cultures of 160 non-pathogenic fungi has shown that 4 cultures produce non protein materials able to lyse plasma clots and fibrin, both human and bovine source; at least one shows some specificity against human plasma clots.
The role of 44-methylgambierone in ciguatera fish poisoning: Acute toxicity, production by marine microalgae and its potential as a biomarker for Gambierdiscus spp. (2020)

Ciguatera fish poisoning (CFP) is prevalent around the tropical and sub-tropical latitudes of the world and impacts many Pacific island communities intrinsically linked to the reef system for sustenance and trade. While the genus Gambierdiscus has been linked with CFP, it is commonly found on tropical reef systems in microalgal assemblages with other genera of toxin-producing, epiphytic and/or benthic dinoflagellates - Amphidinium, Coolia, Fukuyoa, Ostreopsis and Prorocentrum. Identifying a biomarker compound that can be used for the early detection of Gambierdiscus blooms, specifically in a mixed microalgal community, is paramount in enabling the development of management and mitigation strategies. Following on from the recent structural elucidation of 44-methylgambierone, its potential to contribute to CFP intoxication events and applicability as a biomarker compound for Gambierdiscus spp. was investigated. The acute toxicity of this secondary metabolite was determined by intraperitoneal injection using mice, which showed it to be of low toxicity, with an LD<sub>50</sub> between 20 and 38 mg kg<sup>-1</sup>. The production of 44-methylgambierone by 252 marine microalgal isolates consisting of 90 species from 32 genera across seven classes, was assessed by liquid chromatography-tandem mass spectrometry. It was discovered that the production of this secondary metabolite was ubiquitous to the eight Gambierdiscus species tested, however not all isolates of G. carpenteri, and some species/isolates of Coolia and Fukuyoa.
Prediction of Mutagenicity of Organic Molecules by Ensemble Learning (2011)

本研究では、有機化合物の変異原性を予測するためのクラス分類モデルの構築を行った。変異原性を評価するための標準的な方法である復帰突然変異試験を対象とし、その評価結果を高い精度で予測することの出来るモデルの構築を目指した。クラス分類モデル構築のための手法として、複数のSupport Vector Machine（SVM）モデルをサブモデルとして構築し、それらを組み合わせることで予測を行うアンサンブル手法を提案する。データセットから一部の化合物および構造記述子をランダムに抜き出し、SVMを用いてサブモデルを構築する。このとき、SVMのパラメータについても乱数によって無作為に決定する。この操作を複数回繰り返した後、精度の高いサブモデルの予測結果を統合することで変異原性の予測を行う。Hansenら[K. Hansen, et al., J. Chem. Inf. Model., 49, 2077-2081] が収集・整理した、6,512化合物からなる復帰突然変異試験のデータセットを用い、モデルの構築および評価を行った。その結果、テストセットに対する予測正解率79.6%のモデルを構築することに成功した。これは、通常のSVMによって得られるモデルと比較し高い精度を示すものであった。また、The Area Under ROC-Curve（AUC）は0.866であり、Hansenらの結果と同等以上の結果であることが確認された。これらのことから、変異原性の予測にあたってはSVMおよびアンサンブルモデルを用いることが有力であるとの結論が得られた。
Ghost Machine: A Distributed Virtual Machine Architecture for Mobile Java Applications (1998)

The Ghost Machine platform lets you run a limited subset of Java on mobile computing devices. Because it supports a true Java subset, the same programs can also be compiled and run on any fully-implemented Java platform. The Ghost Machine platform currently supports PalmOS devices such as the PalmPilot. It has been designed with special consideration given to memory footprint and efficiency.
Gardening in Your Apartment : Creating an Interior Oasis (1996)

A gardening manual written for those living in flats which outlines the design options, from displaying plants to best effect to choosing plants for their colour and scent, and provides advice on how to mark the changing seasons indoors with both flowering and edible plants.
Ring‐Opening Polymerization of Prodrugs: A Versatile Approach to Prepare Well‐Defined Drug‐Loaded Nanoparticles (2014)

Abstract The synthesis of polymer–drug conjugates from prodrug monomers consisting of a cyclic polymerizable group that is appended to a drug through a cleavable linker is achieved by organocatalyzed ring‐opening polymerization. The monomers polymerize into well‐defined polymer prodrugs that are designed to self‐assemble into nanoparticles and release the drug in response to a physiologically relevant stimulus. This method is compatible with structurally diverse drugs and allows different drugs to be copolymerized with quantitative conversion of the monomers. The drug loading can be controlled by adjusting the monomer(s)/initiator feed ratio and drug release can be encoded into the polymer by the choice of linker. Initiating these monomers from a poly(ethylene glycol) macroinitiator results in amphiphilic diblock copolymers that spontaneously self‐assemble into micelles with a long plasma circulation, which is useful for systemic therapy.
Sampling-Based Subnetwork Identification from Microarray Data and Protein-Protein Interaction Network (2012)

Identification of condition-specific protein interaction subnetworks has emerged as an attractive research field to reveal molecular mechanisms of diseases and provide reliable network biomarkers for disease diagnosis. Several methods have been proposed, which integrate gene expression and protein-protein interaction (PPI) data to identify subnetworks. However, existing methods treat differential expression of genes and network topology independently, which is an oversimplified assumption to model real biological systems. In this paper, we propose a sampling-based subnetwork identification approach to take into account the dependency between gene expression and network topology. Specifically, we apply Markov random field (MRF) theory to model the dependency of genes in PPI network using a Bayesian framework, followed by a Markov Chain Monte Carlo (MCMC) approach to identify significant subnetworks. The MCMC approach estimates the posterior distribution of genes' significant scores and network structure iteratively. Experimental results on both synthetic data and real breast cancer data demonstrated the effectiveness of the proposed method in identifying subnetworks, especially several functionally important, aberrant subnetworks associated with pathways involved in the development and recurrence of breast cancer.