nils-herrmann/clean_scirepeval huggingface dataset:
Using Mapreduce for Efficient Parallel Processing of Continuous K nearest Neighbors in Road Networks

The problem of searching the continuous k Nearest Neighbor (CkNN) objects in road networks is a major challenge due to the highly dynamic nature of the road network environment. Also, the fast increasing number of moving objects poses a big challenge to the CkNN search of moving objects. In addition, it is important to deliver a valid response to the user in an optimal time while taking into account the large volume of data and the amount of changes in the characteristics of moving objects. To effectively explore the search space as well as reduce the time spent to deliver a response to the user, we propose to combine the strengths of Formal Concept Analysis (FCA) as a powerful mean of clustering the moving objects related information, and the processing capabilities of MapReduce, as a well known parallel programming model. The mathematical foundation of FCA allows offering an abstraction of the network based on the neighborhoods. We build the concept lattice based on the binary relations between the target points as well as their properties. The latter are collected from various sensors on the road network. We also propose a density based road network partitioning approach and MapReduce function to distribute the search tasks. Finally, an implementation based on the Storm parallel programming model is discussed to show the effectiveness of our FCA based solution.
Testing Point Null Hypothesis of a Normal Mean and the Truth: 21st Century Perspective

Testing a point (sharp) null hypothesis is arguably the most widely used statistical inferential procedure in many fields of scientific research, nevertheless, the most controversial, and misapprehended. Since 1935 when Buchanan Wollaston raised the first criticism against hypothesis testing, this foundational field of statistics has drawn increasingly active and stronger opposition, including draconian suggestions that statistical significance testing should be abandoned or even banned. Statisticians should stop ignoring these accumulated and significant anomalies within the current point null hypotheses paradigm and rebuild healthy foundations of statistical science. The foundation for a paradigm shift in testing statistical hypotheses is suggested, which is testing interval null hypotheses based on implications of the Zero probability paradox. It states that in a real world research point null hypothesis of a normal mean has zero probability. This implies that formulated point null hypothesis of a mean in the context of the simple normal model is almost surely false. Thus, Zero probability paradox points to the root cause of so called large n problem in significance testing. It discloses that there is no point in searching for a cure under the current point null paradigm. paradigm shift in testing statistical hypotheses. " It cannot be denied that, during the recent rapid development of practical methods, fundamental problems have been ignored and fundamental paradoxes left unresolved " Fisher (1922)
Predictive wind turbine simulation with an adaptive lattice Boltzmann method for moving boundaries

Operating horizontal axis wind turbines create large scale turbulent wake structures that affect the power output of downwind turbines considerably. The computational prediction of this phenomenon is challenging as efficient low dissipation schemes are necessary that represent the vorticity production by the moving structures accurately and that are able to transport wakes without significant artificial decay over distances of several rotor diameters. We have developed a parallel adaptive lattice Boltzmann method for large eddy simulation of turbulent weakly compressible flows with embedded moving structures that considers these requirements rather naturally and enables first principle simulations of wake turbine interaction phenomena at reasonable computational costs. The paper describes the employed computational techniques and presents validation simulations for the Mexnext benchmark experiments as well as simulations of the wake propagation in the Scaled Wind Farm Technology (SWIFT) array consisting of three Vestas V27 turbines in triangular arrangement.
Implementation issues and benchmarking of lattice Boltzmann method for moving rigid particle simulations in a viscous flow
Venue: Comput. Math. Appl.

In this work, we revisit implementation issues in the lattice Boltzmann method (LBM) concerning moving rigid solid particles suspended a viscous fluid. Three aspects relevant to the interaction between flow of a viscous fluid and moving solid boundaries are considered. First, the popular interpolated bounce back scheme is examined both theoretically and numerically. It is important to recognize that even though significant efforts had previously been devoted to the performance, especially the accuracy, of different interpolated bounce back schemes for a fixed boundary, there were relatively few studies focusing on moving solid surfaces. In this study, different interpolated bounce back schemes are compared theoretically for a moving boundary. Then, several benchmark cases are presented to show their actual performance in numerical simulations. Second, we examine different implementations of the momentum exchange method to calculate hydrodynamic force and torque acting on a moving surface. The momentum exchange method is well established for fixed solid boundaries, however, for moving solid boundaries there are still open issues such as unphysical force fluctuations and Galilean invariance errors. Recent progress in this direction is discussed, along with our own interpretations and modifications. Several benchmark cases, including a particle laden turbulent channel flow, are used to demonstrate the effects of different modifications on the accuracy and physical results under different physical configurations. The third aspect is the refilling scheme for constructing the unknown distribution functions for the new fluid nodes that emerge from the previous solid region as a particle moves relative to a fixed lattice grid. We examine and compare the performance of the refilling schemes introduced by Fang etzal. (2002) Lallemand and Luo (2003) and Caiazzo (2008) We demonstrate that improvements can be made to suppress force fluctuations resulting from refilling.
A Mathematical Investigation of Vaccination Strategies to Prevent a Measles Epidemic

The purpose of this project is to quantitatively investigate vaccination strategies to prevent measles epidemics. A disease model which incorporates susceptible, vaccinated, infected, and recovered populations (SVIR) is used to investigate the process of how an epidemic of measles can spread within a closed population where a portion of the population has been vaccinated. The model is used to predict the number of infections and resulting reproductive number for the measles based on a variety of initial vaccination levels. The model is further used to investigate the concept of herd immunity, which states that if a certain percentage of the population is vaccinated then it will provide protection for the entire population. Results generated from these modeling efforts suggest that approximately 95\ of the population should be vaccinated against the measles in order to establish a herd immunity.
Unhedgeable Risk: How climate change sentiment impacts investment

Short term shifts in market sentiment induced by awareness of future, as yet unrealised, climate risks could lead to economic shocks, causing substantial losses in financial portfolio value within timescales that are relevant to all investors. Factors, including climate change policy, technological change, asset stranding, weather events and longerterm physical impacts may lead to financial tipping points for which investors are not presently prepared. This research shows that changing asset allocations among various asset classes and regions, combined with investing in sectors exhibiting low climate risk, can offset only half of the negative impacts on financial portfolios brought about by climate change. Climate change thus entails "unhedgeable risk" for investment portfolios. While the response to action aimed at limiting warming below 2degC is shown to be negative in its short term economic and financial impacts, the benefits of early action lead to significantly higher economic growth rates and returns over the long run, especially when compared to a worst case scenario of inaction. The present study shows that certain types of portfolio benefit more than others. Even in the short run, the perception of climate change represents an aggregate risk driver that must be taken into consideration when assessing the performance of asset portfolios. Our analysis provides investors with a general guide to minimising their exposure to climate sentiment risk and has the potential to stimulate a constructive dialogue between investors, governments and regulators to examine the conditions necessary to build more resilient financial markets under unprecedented environmental change.
Teacher Questioning Strategies in Mathematical Classroom Discourse: A Case Study of Two Grade Eight Teachers in Tennessee, USA

Teacher questioning in mathematics is an important diagnostic tool for teaching as well as measuring the academic progression and comprehension of the learner. While teacher questioning enhances student learning and self assessment of the teacher's lesson delivery effectiveness, if not presented properly can have negative impacts on the student learning process. Identifying "good" and/or "effective" questioning strategies is a major challenge to mathematics teachers. To increase teacher effectiveness and student success in mathematics, a self assessment of teacher questioning techniques is essential. This study examines the questioning strategies used by two grade 8 teachers, selected at random, from twelve middle school teachers each handling quadratic mathematical modeling as one of their lessons in a project. The purpose of this study was to determine the questioning strategies used by the two teachers in their mathematical classroom discourse. Each class was videotaped over six month period but only a section from each of the two selected classes, on quadratic modeling, was watched for about 45 minutes long for the purpose of this paper. A common theme "teacher questioning strategies" was the bases for analyzing the data. The strategies include: probing and follow up, leading, check listing and student specific questioning. Findings from the study indicate that guiding teachers (pre service and in service) through an analysis of questions they ask and the responses they get from students during mathematical discourse, may enable them recognize both effective and ineffective questioning strategies in their mathematical classroom discourse. This study may help both pre service and in service teachers as well as teacher researchers to be well aware of their questioning practices by reflecting on the questioning strategies they use in their own mathematical classroom discourse.  probing and follow up, scaffolding, checklisting strategy, leading questions, student specific questioning
Optimizing Treatment of Complicated Grief: A Randomized Clinical Trial.
Venue: JAMA psychiatry

To our knowledge, this is the first placebo controlled randomized clinical trial to evaluate the efficacy of antidepressant pharmacotherapy, with and without complicated grief psychotherapy, in the treatment of complicated grief.  To confirm the efficacy of a targeted complicated grief treatment (CGT) determine whether citalopram (CIT) enhances CGT outcome, and examine CIT efficacy without CGT.  Included in the study were 395 bereaved adults who met criteria for CG recruited from March 2010 to September 2014 from academic medical centers in Boston, Massachusetts; New York, New York; Pittsburgh, Pennsylvania; and San Diego, California. Co occurring substance abuse, psychosis, mania, and cognitive impairment were exclusionary. Study participants were randomized using site specific permuted blocks stratified by major depression into groups prescribed CIT (n 101) placebo (PLA; n 99) CGT with CIT (n 99) and CGT with PLA (n 96) Independent evaluators conducted monthly assessments for 20 weeks. Response rates were compared under the intention to treat principle, including all randomized participants in a logistic regression with inverse probability weighting.  All participants received protocolized pharmacotherapy optimized by flexible dosing, psychoeducation, grief monitoring, and encouragement to engage in activities. Half were also randomized to receive manualized CGT in 16 concurrent weekly sessions.  Complicated grief anchored Clinical Global Impression scale measurments every 4 weeks. Response was measured as a rating of "much improved" or "very much improved."  Of the 395 study participants, 308 (78.0% were female and 325 (82.3% were white. Participants' response to CGT with PLA vs PLA (82.5% vs 54.8% relative risk [RR] 1.51; 95% CI, 1.16 1.95; P .002; number needed to treat [NNT] 3.6) suggested the efficacy of CGT, and the addition of CIT did not significantly improve CGT outcome (CGT with CIT vs CGT with PLA: 83.7% vs 82.5% RR, 1.01; 95% CI, 0.88 1.17; P .84; NNT, 84) However, depressive symptoms decreased significantly more when CIT was added to treatment (CGT with CIT vs CGT with PLA: model based adjusted mean [standard error] difference, 2.06 [1.00] 95% CI, 4.02 to 0.11; P .04) By contrast, adding CGT improved CIT outcome (CIT vs CGT with CIT: 69.3% vs 83.7% RR, 1.21; 95% CI, 1.00 1.46; P .05; NNT, 6.9) Last, participant response to CIT was not significantly different from PLA at week 12 (45.9% vs 37.9% RR, 1.21; 95% CI, 0.82 1.81; P .35; NNT, 12.4) or at week 20 (69.3% vs 54.8% RR, 1.26; 95% CI, 0.95 1.68; P .11; NNT, 6.9) Rates of suicidal ideation diminished to a substantially greater extent among participants receiving CGT than among those who did not.  Complicated grief treatment is the treatment of choice for CG, and the addition of CIT optimizes the treatment of co occurring depressive symptoms.
NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down Regulates Immune Response and Cancer Promotion Genes
Venue: PloS one

Regulation of gene expression is one of several roles proposed for the stress induced nucleotide diadenosine tetraphosphate (Ap4A) We have examined this directly by a comparative RNA Seq analysis of KBM 7 chronic myelogenous leukemia cells and KBM 7 cells in which the NUDT2 Ap4A hydrolase gene had been disrupted (NuKO cells) causing a 175 fold increase in intracellular Ap4A. 6,288 differentially expressed genes were identified with P 0.05. Of these, 980 were up regulated and 705 down regulated in NuKO cells with a fold change 2.  Pathway Analysis (IPA(r) was used to assign these genes to known canonical pathways and functional networks. Pathways associated with interferon responses, pattern recognition receptors and inflammation scored highly in the down regulated set of genes while functions associated with MHC class II antigens were prominent among the up regulated genes, which otherwise showed little organization into major functional gene sets. Tryptophan catabolism was also strongly down regulated as were numerous genes known to be involved in tumor promotion in other systems, with roles in the epithelial mesenchymal transition, proliferation, invasion and metastasis. Conversely, some pro apoptotic genes were up regulated. Major upstream factors predicted by IPA(r) for gene down regulation included NFkB, STAT1/2, IRF3/4 and SP1 but no major factors controlling gene up regulation were identified. Potential mechanisms for gene regulation mediated by Ap4A and/or NUDT2 disruption include binding of Ap4A to the HINT1 co repressor, autocrine activation of purinoceptors by Ap4A, chromatin remodeling, effects of NUDT2 loss on transcript stability, and inhibition of ATP dependent regulatory factors such as protein kinases by Ap4A. Existing evidence favors the last of these as the most probable mechanism. Regardless, our results suggest that the NUDT2 protein could be a novel cancer chemotherapeutic target, with its inhibition potentially exerting strong anti tumor effects via multiple pathways involving metastasis, invasion, immunosuppression and apoptosis.
A Survey on Intrusion Detection System: State of the Art Review

To analyze and monitoring the activity of nodes using an IDS Intrusion Detection System which provide security to the system.  In this research, a network building was made with simple node formation with a fitting technique. So that it is easy for a user or beginner to understand the asymptotic dominion factors, due to the wide growth of nodes on network. Intrusion detection system is made of several nodes. These nodes are grouped and combined as a network. Since each node in a network has unique characteristics they may have high chance of attack from malware during the communication between systems.  Network of topology is done by creating and connecting various sub networks. Sub networks traffic is cleared and monitored with the package of IDS. It works on synchronous message transfer mode which provides acknowledgement to sender and receiver. All sub networks is managed by its corresponding system and further provide update to the master node on the network. Due to this broadcast of messages all other nodes may be in safe state of avoidance from attacker.
Tumor information extraction in radiology reports for hepatocellular carcinoma patients
Venue: CRI

Hepatocellular carcinoma (HCC) is a deadly disease affecting the liver for which there are many available therapies. Targeting treatments towards specific patient groups necessitates defining patients by stage of disease. Criteria for such stagings include information on tumor number, size, and anatomic location, typically only found in narrative clinical text in the electronic medical record (EMR) Natural language processing (NLP) offers an automatic and scale able means to extract this information, which can further evidence based research. In this paper, we created a corpus of 101 radiology reports annotated for tumor information. Afterwards we applied machine learning algorithms to extract tumor information. Our inter annotator partial match agreement scored at 0.93 and 0.90 F1 for entities and relations, respectively. Based on the annotated corpus, our sequential labeling entity extraction achieved 0.87 F1 partial match, and our maximum entropy classification relation extraction achieved scores 0.89 and 0. 74 F1 with gold and system entities, respectively.
Dispersion Corrected Mean Field Electronic Structure Methods.
Venue: Chemical reviews

Mean field electronic structure methods like Hartree Fock, semilocal density functional approximations, or semiempirical molecular orbital (MO) theories do not account for long range electron correlation (London dispersion interaction) Inclusion of these effects is mandatory for realistic calculations on large or condensed chemical systems and for various intramolecular phenomena (thermochemistry) This Review describes the recent developments (including some historical aspects) of dispersion corrections with an emphasis on methods that can be employed routinely with reasonable accuracy in large scale applications. The most prominent correction schemes are classified into three groups: (i) nonlocal, density based functionals, (ii) semiclassical C6 based, and (iii) one electron effective potentials. The properties as well as pros and cons of these methods are critically discussed, and typical examples and benchmarks on molecular complexes and crystals are provided. Although there are some areas for further improvement (robustness, many body and short range effects) the situation regarding the overall accuracy is clear. Various approaches yield long range dispersion energies with a typical relative error of 5% For many chemical problems, this accuracy is higher compared to that of the underlying mean field method (i.e. a typical semilocal (hybrid) functional like B3LYP)
Synovial Joints and Lubrication Mechanisms

Synovial joints form the most important feature of the human body as they represent the centers of the most essential and basic activity in the human beings, which is motion. A synovial joint can be described as a load carrying system consisting of two mating bones with tangential and /or normal motions. The bone ends, which are usually spherical in appearance, are covered with a soft sponge like material, called articular cartilage. The space between these cartilaginous extremities of the bones, known as joint cavity, is filled with a sheardependent fluid called synovial fluid. The surfaces of the synovial joints have a high degree of geometrical conformity.
Implementation of a PSoC based flexible and low power processor
Venue: 2016 24th Iranian Conference on Electrical Engineering (ICEE)

A flexible and low power PSoC basecd platform has been implemented for discrete wavelet transform (DWT) and Fast Fourier transform (FFT) applications. Our designs comprise 1024 point FFT and 5 stage parametric DWT and digital filter processing units. High accuracy, low power consumption, flexibility and minimal hardware resource usage are characteristics of this design. This portable processor has been implemented on CY8C5868AXI LP035 from PSoC5LP (ARM Cortex M3) Cypress family. Total power consumption of the design for DWT and FFT is 90 mW and 38.35mW respectively in 67MHZ frequency which is an appropriate value when compared with ASIC, FPGA and DSP based structures. The designed structure has high accuracy in computation, so that the maximum error is about 0.04 compared with the actual results.
Mobile payments: a scoping study of the literature and issues for future research

Despite its huge potential, the use of mobile technology for carrying out payment transactions and replicating monetary features, has only taken off in a limited number of countries. The fact that mobile payment services are not being provided on a worldwide scale, suggests that the reasons for the successful cases are not yet fully understood, and as a result, cannot be easily replicated. This paper seeks to fill this knowledge gap by providing a comprehensive scoping study, which seeks to map out the literature published between 2001 and 2011. An investigation has been carried out of a total of 94 peer reviewed papers, with the aim of providing a comprehensive picture of the knowledge, production and dissemination about mobile payments. Furthermore, this study includes a detailed analysis of 12 primary case studies on existing mobile payment schemes, as well as a consultation exercise with stakeholders. The main contribution of this study is to provide a clear account of the knowledge that exists on mobile payments. As a result, it has been possible to detect serious gaps in this knowledge base (in geographical, methodological and conceptual areas) and show how future research can make improvements in the field.