Large-scale Comparison Research Articles

Supplement Materials of the article "Large-scale comparison of machine learning algorithms for target prediction of natural products".

Supplement Materials of the article "Large-scale comparison of machine learning algorithms for target prediction of natural products".

Text complexity and linguistic features: Their correlation in English and Russian

Text complexity assessment is a challenging task requiring various linguistic aspects to be taken into consideration. The complexity level of the text should correspond to the reader’s competence. A too complicated text could be incomprehensible, whereas a too simple one could be boring. For many years, simple features were used to assess readability, e.g. average length of words and sentences or vocabulary variety. Thanks to the development of natural language processing methods, the set of text parameters used for evaluating readability has expanded significantly. In recent years, many articles have been published the authors of which investigated the contribution of various lexical, morphological, and syntactic features to the readability level. Nevertheless, as the methods and corpora are quite diverse, it may be hard to draw general conclusions as to the effectiveness of linguistic information for evaluating text complexity due to the diversity of methods and corpora. Moreover, a cross-lingual impact of different features on various datasets has not been investigated. The purpose of this study is to conduct a large-scale comparison of features of different nature. We experimentally assessed seven commonly used feature types (readability, traditional features, morphological features, punctuation, syntax frequency, and topic modeling) on six corpora for text complexity assessment in English and Russian employing four common machine learning models: logistic regression, random forest, convolutional neural network and feedforward neural network. One of the corpora, the corpus of fiction literature read by Russian school students, was constructed for the experiment using a large-scale survey to ensure the objectivity of the labeling. We showed which feature types can significantly improve the performance and analyzed their impact according to the dataset characteristics, language, and data source.

A large-scale comparison of the grid impact of centralized and decentralized charge control for electric vehicles

The global goal for a significant reduction of carbon emissions in the mobility sector is accompanied by an increasing market penetration of electric vehicles (EV). As a result of this, distribution grids see a change in power demand. This contribution investigates and compares different decentralized and centralized EV charging control approaches with respect to their grid impacts and user satisfaction. The focus of this analysis is the utilization of different types of reactive power management using heuristic problem optimization for chargers. A large-scale MV and LV grid simulation framework is developed and combined with an EV simulation. Parameters such as transformer and line loading, losses, voltage profiles and voltage band violations as well as the reached fleet state of charge (SOC) are considered. The comparison of the implemented scenarios shows that a decentralized reactive power injection combined with potential active power curtailment results in the best EV integration.

The evolutionary trajectory of drosophilid walking

Neural circuits must both execute the behavioral repertoire of individuals and account for behavioral variation across species. Understanding how this variation emerges over evolutionary time requires large-scale phylogenetic comparisons of behavioral repertoires. Here, we describe the evolution of walking in fruit flies by capturing high-resolution, unconstrained movement from 13 species and 15 strains of drosophilids. We find that walking can be captured in a universal behavior space, the structure of which is evolutionarily conserved. However, the occurrence of and transitions between specific movements have evolved rapidly, resulting in repeated convergent evolution in the temporal structure of locomotion. Moreover, a meta-analysis demonstrates that many behaviors evolve more rapidly than other traits. Thus, the architecture and physiology of locomotor circuits can execute precise individual movements in one species and simultaneously support rapid evolutionary changes in the temporal ordering of these modular elements across clades.

Digital divides in access and use in literacy instruction in rural high schools

• Literacy instruction in rural schools varies widely in terms of technology use and access. • Large-scale quantitative studies fail to capture differences between local contexts. • Teacher technology training is essential but difficult to implement in rural schools. This article presents institutional case studies of technology use in language and literacy instruction at two rural high schools based on almost two months of classroom observations as well as interviews with teachers, administrators, and students. The first school presented faced a number of funding issues and clearly lacked in terms of access—the teachers regularly expressed frustration with district leadership and lamented their ability to have students do more computer-based literacy work. The second school presented had a very different issue—through a series of grants, they had secured computers for every student in their English classes but teachers had varying level of training on how to incorporate them in learning and consequently, the computers were often used in reductive ways. This research provides a perspective that shows the limitations of large-scale comparisons, emphasizing how local contextual factors (such as school leadership and teacher training) can shape both access and use. It also shows how access is only one piece of the picture—without sufficient teacher training and support, available technology may help perpetuate reductive educational practices in language and literacy instruction .

Effect of a proactive esophageal cooling device on procedure length - a multicenter comparison of persistent and paroxysmal atrial fibrillation

Abstract Funding Acknowledgements Type of funding sources: None. Background During left atrial ablation for the treatment of atrial fibrillation (AF), effective esophageal protection is essential for reducing or preventing thermal injury. Traditional methods include luminal esophageal temperature (LET) monitoring that lead to frequent pauses in the procedure when temperature alarms alert operators to dangerous temperature levels. While there have been recent studies that demonstrate an association between active esophageal cooling and a reduction in procedure duration regardless of AF type, these retrospective studies have been conducted at single or joint centers which may lead to confounding from other time-saving variables that have changed over time. Purpose Consequently, we sought to perform a large-scale multicenter comparison to better elucidate the association between procedure length and the use of active cooling in patients with persistent and paroxysmal atrial fibrillation. Methods In this study, we collected data from three large hospital centers, one hospital-maintained registry, one physician-maintained registry, and one through EHR data review and aggregated in groups separated by AF type as well as whether the patients received active cooling or LET monitoring. We then compared median procedure durations in each group. Results There were a total of 753 patients included in this study. Of the 360 patients with paroxysmal AF, 179 received active esophageal cooling while 181 underwent LET monitoring. In the persistent AF group with 393 patients, 157 received active esophageal cooling and 236 underwent LET monitoring. Among patients with paroxysmal AF, the median mean procedure duration was 137 minutes in the LET monitored group, and 90 minutes in the actively cooled group with an overall reduction of 47 minutes (P<.001). In patients with persistent AF, the median procedure duration was 148 minutes in the LET monitored group and 94 minutes in the actively cooled group with an overall reduction of 54 minutes (P<.001). The relative reduction as a percent of total procedure time was 34%, and 36%, for paroxysmal and persistent AF cases, respectively. Conclusion In this large multicenter review, there is a significant reduction in procedure length when using active esophageal cooling, regardless of AF type.

Lipid pathway dysfunction is prevalent in patients with Parkinson's disease.

Many genetic risk factors for Parkinson’s disease have lipid-related functions and lipid-modulating drugs such as statins may be protective against Parkinson’s disease. Moreover, the hallmark Parkinson’s disease pathological protein, α-synuclein, has lipid membrane function and pathways dysregulated in Parkinson’s disease such as the endosome–lysosome system and synaptic signalling rely heavily on lipid dynamics. Despite the potential role for lipids in Parkinson’s disease, most research to date has been protein-centric, with large-scale, untargeted serum and CSF lipidomic comparisons between genetic and idiopathic Parkinson’s disease and neurotypical controls limited. In particular, the extent to which lipid dysregulation occurs in mutation carriers of one of the most common Parkinson’s disease risk genes, LRRK2, is unclear. Further, the functional lipid pathways potentially dysregulated in idiopathic and LRRK2 mutation Parkinson’s disease are underexplored.To better determine the extent of lipid dysregulation in Parkinson’s disease, untargeted high-performance liquid chromatography–tandem mass spectrometry was performed on serum (n = 221) and CSF (n = 88) obtained from a multi-ethnic population from the Michael J. Fox Foundation LRRK2 Clinical Cohort Consortium. The cohort consisted of controls, asymptomatic LRRK2 G2019S carriers, LRRK2 G2019S carriers with Parkinson’s disease and Parkinson’s disease patients without a LRRK2 mutation. Age and sex were adjusted for in analyses where appropriate. Approximately 1000 serum lipid species per participant were analysed.The main serum lipids that distinguished both Parkinson’s disease patients and LRRK2 mutation carriers from controls included species of ceramide, triacylglycerol, sphingomyelin, acylcarnitine, phosphatidylcholine and lysophosphatidylethanolamine. Significant alterations in sphingolipids and glycerolipids were also reflected in Parkinson’s disease and LRRK2 mutation carrier CSF, although no correlations were observed between lipids identified in both serum and CSF. Pathway analysis of altered lipid species indicated that sphingolipid metabolism, insulin signalling and mitochondrial function were the major metabolic pathways dysregulated in Parkinson’s disease. Importantly, these pathways were also found to be dysregulated in serum samples from a second Parkinson’s disease cohort (n = 315).Results from this study demonstrate that dysregulated lipids in Parkinson’s disease generally, and in LRRK2 mutation carriers, are from functionally and metabolically related pathways. These findings provide new insight into the extent of lipid dysfunction in Parkinson’s disease and therapeutics manipulating these pathways may be beneficial for Parkinson’s disease patients. Moreover, serum lipid profiles may be novel biomarkers for both genetic and idiopathic Parkinson’s disease.

Complete Genome Sequences of Four Strains ofErwiniatracheiphila: A Resource for Studying aBacterial Plant Pathogen with a Highly Complex Genome.

Complete Genome Sequences of Four Strains ofErwiniatracheiphila: A Resource for Studying aBacterial Plant Pathogen with a Highly Complex Genome.

Pericardiocentesis or surgical drainage: A national comparison of clinical outcomes and resource use.

BackgroundWhile institutional series have sought to define the optimal strategy for drainage of pericardial effusions, large-scale comparisons remain lacking. Using a nationally representative sample, the present study examined clinical and financial outcomes following pericardiocentesis (PC) and surgical drainage (SD) in patients admitted for pericardial effusion and tamponade.MethodsAdults undergoing PC or SD within 2 days of admission for non-surgically related pericardial effusion or tamponade were identified in the 2016–2019 Nationwide Readmissions Database. Multivariable logistic and linear models were developed to evaluate the association between intervention type and outcomes. The primary outcome of interest was mortality while secondary endpoints included reintervention, periprocedural complications, hospital length of stay (LOS), hospitalization costs and 30-day non-elective readmission.ResultsOf an estimated 44,637 records meeting inclusion criteria, 28,862 (64.7%) underwent PC while the remainder underwent SD for initial management of pericardial effusion or tamponade. PC was associated with significantly increased odds of in-hospital mortality, reintervention and 30-day readmission relative to SD. PC was also associated with greater odds of cardiac complications but lower odds of infection, respiratory failure and blood transfusions compared to SD. Although PC was associated with shorter index hospital length of stay and costs, the two strategies yielded similar 30-day cumulative costs.ConclusionManagement of pericardial effusion with PC is associated with greater odds of mortality, reintervention and 30-day readmission but similar 30-day cumulative costs compared to SD. In the setting of adequate hospital capability and operator expertise, SD is a reasonable initial treatment strategy for pericardial effusion.

A General Pairwise Comparison Model for Extremely Sparse Networks

Statistical estimation using pairwise comparison data is an effective approach to analyzing large-scale sparse networks. In this article, we propose a general framework to model the mutual interactions in a network, which enjoys ample flexibility in terms of model parameterization. Under this setup, we show that the maximum likelihood estimator for the latent score vector of the subjects is uniformly consistent under a near-minimal condition on network sparsity. This condition is sharp in terms of the leading order asymptotics describing the sparsity. Our analysis uses a novel chaining technique and illustrates an important connection between graph topology and model consistency. Our results guarantee that the maximum likelihood estimator is justified for estimation in large-scale pairwise comparison networks where data are asymptotically deficient. Simulation studies are provided in support of our theoretical findings. Supplementary materials for this article are available online.

A large-scale comparison of reproduction and recruitment of the stalked barnacle Pollicipes pollicipes across Europe

Understanding large-scale spatial and temporal patterns of marine populations is a central goal in ecology, which has received renewed attention under climate change. However, few studies explore the large-scale dynamics of populations using standardized protocols and during the same time frames. We studied the phenology and intensity of reproduction and recruitment for the intertidal stalked barnacle Pollicipes pollicipes over an European scale and described their potential linkages with environmental variables. This species supports profitable fisheries in the Iberian Peninsula (Spain and Portugal). In Brittany (France), we had observed a significant lower reproductive effort (long non-breeding season, short breeding period in summer) and low values of recruitment intensity. This pattern may be related to the fact that Brittany corresponds to the northern limit of the distribution of this species in continental Europe. On the Iberian Peninsula, the most different region was Galicia (Spain), with Asturias (Spain) and SW Portugal being more similar. In Galicia, we have observed a contradictory pattern characterized by the absence of a non-breeding period and by a shorter recruitment season than observed in other Iberian regions. Our results suggest that air temperature, SST and chlorophyll-a might be related to the variability in reproduction and recruitment patterns of P. pollicipes. Moreover, spring and early summer upwelling in SW Portugal and Galicia might be inhibiting recruitment in this period. At the northern limit, the expected increase in performance under climate change might facilitate the recovery of populations after exploitation, increasing the resilience of the resource to fishing pressure.

Understanding the accuracy of modelled changes in freshwater provision over time

Accurate modelling of changes in freshwater supplies is critical in an era of increasing human demand, and changes in land use and climate. However, there are concerns that current landscape-scale models do not sufficiently capture catchment-level changes, whilst large-scale comparisons of empirical and simulated water yield changes are lacking. Here we modelled annual water yield in two time periods (1: 1985–1994 and 2: 2008–2017) across 81 catchments in England and validated against empirical data. Our objectives were to i) investigate whether modelling absolute or relative change in water yield is more accurate and ii) determine which predictors have the greatest impact on model accuracy. We used the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) Annual Water Yield model. In this study, absolute values refer to volumetric units of million cubic metres per year (Mm3/y), either at the catchment or hectare level.Modelled annual yields showed high accuracy as indicated by the low Mean Absolute Deviation (MAD, based on normalised data, 0 is high and 1 is low accuracy) at the catchment (1: 0.013 ± 0.019, 2: 0.012 ± 0.020) and hectare scales (1: 0.03 ± 0.030, 2: 0.030 ± 0.025). But accuracy of modelled absolute change in water yield showed a more moderate fit on both the catchment (MAD = 0.055 ± 0.065) and hectare (MAD = 0.105 ± 0.089) scales. Relative change had lower accuracy (MAD = 0.189 ± 0.135). Anthropogenic modifications to the hydrological system, including water abstraction contributed significantly to the inaccuracy of change values at the catchment and hectare scales.Quantification of changes in freshwater provision can be more accurately articulated using absolute values rather than using relative values. Absolute values can provide clearer guidance for mitigation measures related to human consumption. Accuracy of modelled change is related to different aspects of human consumption, suggesting anthropogenic impacts are critically important to consider when modelling water yield.

A Large-Scale Comparison of Tetrahedral and Hexahedral Elements for Solving Elliptic PDEs with the Finite Element Method

The Finite Element Method (FEM) is widely used to solve discrete Partial Differential Equations (PDEs) in engineering and graphics applications. The popularity of FEM led to the development of a large family of variants, most of which require a tetrahedral or hexahedral mesh to construct the basis. While the theoretical properties of FEM basis (such as convergence rate, stability, etc.) are well understood under specific assumptions on the mesh quality, their practical performance, influenced both by the choice of the basis construction and quality of mesh generation, have not been systematically documented for large collections of automatically meshed 3D geometries. We introduce a set of benchmark problems involving most commonly solved elliptic PDEs, starting from simple cases with an analytical solution, moving to commonly used test problem setups, and using manufactured solutions for thousands of real-world, automatically meshed geometries. For all these cases, we use state-of-the-art meshing tools to create both tetrahedral and hexahedral meshes, and compare the performance of different element types for common elliptic PDEs. The goal of this benchmark is to enable comparison of complete FEM pipelines, from mesh generation to algebraic solver, and exploration of relative impact of different factors on the overall system performance. As a specific application of our geometry and benchmark dataset, we explore the question of relative advantages of unstructured (triangular/ tetrahedral) and structured (quadrilateral/hexahedral) discretizations. We observe that for Lagrange-type elements, while linear tetrahedral elements perform poorly, quadratic tetrahedral elements perform equally well or outperform hexahedral elements for our set of problems and currently available mesh generation algorithms. This observation suggests that for common problems in structural analysis, thermal analysis, and low Reynolds number flows, high-quality results can be obtained with unstructured tetrahedral meshes, which can be created robustly and automatically. We release the description of the benchmark problems, meshes, and reference implementation of our testing infrastructure to enable statistically significant comparisons between different FE methods, which we hope will be helpful in the development of new meshing and FEA techniques.

A Survey of 6D Object Detection Based on 3D Models for Industrial Applications.

Six-dimensional object detection of rigid objects is a problem especially relevant for quality control and robotic manipulation in industrial contexts. This work is a survey of the state of the art of 6D object detection with these use cases in mind, specifically focusing on algorithms trained only with 3D models or renderings thereof. Our first contribution is a listing of requirements typically encountered in industrial applications. The second contribution is a collection of quantitative evaluation results for several different 6D object detection methods trained with synthetic data and the comparison and analysis thereof. We identify the top methods for individual requirements that industrial applications have for object detectors, but find that a lack of comparable data prevents large-scale comparison over multiple aspects.

Comparative Genomics Reveals Evolutionary Traits, Mating Strategies, and Pathogenicity-Related Genes Variation of Botryosphaeriaceae.

Botryosphaeriaceae, as a major family of the largest class of kingdom fungi Dothideomycetes, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and raw material plants for biofuel production. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted a large-scale whole-genome comparison of 271 Dothideomycetes, including 19 species in Botryosphaeriaceae. The comparative genome analysis provided a clear classification of Botryosphaeriaceae in Dothideomycetes and indicated that the evolution of lifestyle within Dothideomycetes underwent four major transitions from non-phytopathogenic to phytopathogenic. Mating strategies analysis demonstrated that at least 3 transitions were found within Botryosphaeriaceae from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different genera varied greatly, indicative of genus-lineage expansion within Botryosphaeriaceae. These findings shed new light on evolutionary traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae.

Large-scale comparison of machine learning algorithms for target prediction of natural products

Large-scale comparison of machine learning algorithms for target prediction of natural products

Genotype-Phenotype Comparison in POGZ-Related Neurodevelopmental Disorders by Using Clinical Scoring.

POGZ-related disorders (also known as White-Sutton syndrome) encompass a wide range of neurocognitive abnormalities and other accompanying anomalies. Disease severity varies widely among POGZ patients and studies investigating genotype-phenotype association are scarce. Therefore, our aim was to collect data on previously unreported POGZ patients and perform a large-scale phenotype-genotype comparison from published data. Overall, 117 POGZ patients’ genotype and phenotype data were included in the analysis, including 12 novel patients. A severity scoring system was developed for the comparison. Mild and severe phenotypes were compared with the types and location of the variants and the predicted presence or absence of nonsense-mediated RNA decay (NMD). Missense variants were more often associated with mild phenotypes (p = 0.0421) and truncating variants predicted to escape NMD presented with more severe phenotypes (p < 0.0001). Within this group, variants in the prolin-rich region of the POGZ protein were associated with the most severe phenotypes (p = 0.0004). Our study suggests that gain-of-function or dominant negative effect through escaping NMD and the location of the variants in the prolin-rich domain of the protein may play an important role in the severity of manifestations of POGZ–associated neurodevelopmental disorders.

Large-scale comparison between the diffraction-component precision indexes favors Cruickshank’s Rfree function

This study aims to provide a first large-scale comparison between the various diffraction-component precision index (DPI) equations, assess the applicability of the parameter, and make recommendations on DPI computation. The DPI estimates the average accuracy of the atomic coordinates obtained by the structural refinement of protein diffraction data, with application in crystallography and cheminformatics. Although, Cruickshank and Blow proposed DPI equations based on R and Rfree in order to calculate DPI values, which remain scarcely employed in the quality assessment of the Protein Data Base (PDB) files, due to the unclear data extraction protocols (to assign variables), the complex equations, the lack of extensive applicability studies and the limited access to automated computations. In order to address these shortcomings, the entire RCSB PDB database was evaluated using Cruickshank?s and Blow?s R and Rfree DPI variations. Computations of 143070 X-ray structures indicate that Rfree-based DPI equations apply to 30 % more protein structures compared to R-based DPI equations, with Cruickshank Rfree-based DPI (CRF) exceeding the number of successful Blow?s Rfree-based DPI (BRF) computations. Although our results indicate that, in general, the resolutions &lt; 2 ? assure consistency among the various DPIs computations (differences &lt;0.05 ?), we recommend the use of CRF DPI because of its wider applicability.

Right-wing Extremist Organizations of Modern Germany: Attempts to Revise History as a Threat to Social Cohesion

The article presents an analysis of the activities of right-wing extremist organizations in Germany aimed at revising the results of the Second World War. Historical revisionism has become a central place of propaganda for German legal extremism since the 1970s. Its goal is not to generate new scientific knowledge, but to be aimed solely at an ideologically motivated rethinking of historical facts. They present events, creating the impression of an unbiased study of a historical source in a little-informed community. In accordance with their worldview, right-wing extremists deny the guilt of Germany in unleashing the Second World War, transferring it to the victorious powers. In modern Germany, the number of supporters of neo-Nazi groups has increased, which is a blow to social cohesion. In order to counteract this, significant work is being carried out by the Federal Office for the Protection of the Constitution, the police and other State structures. A special role is being played by research activities. In 2020 A research institute of social cohesion was established on the basis of eleven higher educational institutions and research institutions. It is a structure funded by the Federal Ministry of Education and Research, located in ten different lands. Almost 200 scientists from different research teams are developing practical proposals that will help solve the social problems of our time, using empirical research and large-scale comparisons. Among the topics that are analyzed and become the basis for the development of practical proposals, the themes of conflict, polarization and populism, as well as anti-Semitism and hate crimes occupy a prominent place.

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups