nils-herrmann/clean_scirepeval huggingface dataset:
Causes vs Benefits in the Evolution of Prey Grouping

The presence of predators alters the evolutionary pressures acting on prey populations, often driving them to engage in new behaviors in order to avoid being the target of an attack. One common antipredator behavior is group formation, which can reduce the odds of any individual prey being the target of a given attack, typically scaling inversely with the number of prey in the group. This “dilution effect” is often hypothesized to be the primary driver of prey group formation as an anti-predator strategy. However, groups may help with predator avoidance in other ways as well. For example, prey behaviors or physical characteristics that visually confuse predators may reduce their ability to target an individual and make a kill. Indeed, some have suggested that the “predator confusion” effect alone is sufficient to drive the evolution of grouping in prey. Here we examine coevolving populations of predators and prey using the Avida digital evolution platform. We evaluate the relative importance of these two potential drivers of the evolution of prey grouping and show that the dilution effect, an inherent property of most prey groups, readily creates the pressures necessary for the evolution of prey grouping. In contrast, we found no evidence that predator confusion plays a significant role in prey group formation. Instead, the dilution effect alone is indicated as the primary driver of antipredator prey grouping strategies.
Analyzing Student Work Patterns Using Programming Exercise Data

Web-based programming exercises are a useful way for students to practice and master essential concepts and techniques presented in introductory programming courses. Although these systems are used fairly widely, we have a limited understanding of how students use these systems, and what can be learned from the data collected by these systems.
 In this paper, we perform a preliminary exploratory analysis of data collected by the CloudCoder programming exercise system from five introductory courses taught in two programming languages across three colleges and universities. We explore a number of interesting correlations in the data that confirm existing hypotheses. Finally, and perhaps most importantly, we demonstrate the effectiveness and future potential of systems like CloudCoder to help us study novice programmers.
Byzantine Chain Replication

We present a new class of Byzantine-tolerant State Machine Replication protocols for asynchronous environments that we term Byzantine Chain Replication. We demonstrate two implementations that present different trade-offs between performance and security, and compare these with related work. Leveraging an external reconfiguration service, these protocols are not based on Byzantine consensus, do not require majoritybased quorums during normal operation, and the set of replicas is easy to reconfigure. One of the implementations is instantiated with t+ 1 replicas to tolerate t failures and is useful in situations where perimeter security makes malicious attacks unlikely. Applied to in-memory BerkeleyDB replication, it supports 20,000 transactions per second while a fully Byzantine implementation supports 12,000 transactions per second—about 70% of the throughput of a non-replicated database.
Pharmacokinetic Drug Interactions Involving Vortioxetine (Lu AA21004), a Multimodal Antidepressant

The identification and quantification of potential drug-drug interactions is important for avoiding or minimizing the interaction-induced adverse events associated with specific drug combinations. Clinical studies in healthy subjects were performed to evaluate potential pharmacokinetic interactions between vortioxetine (Lu AA21004) and co-administered agents, including fluconazole (cytochrome P450 [CYP] 2C9, CYP2C19 and CYP3A inhibitor), ketoconazole (CYP3A and P-glycoprotein inhibitor), rifampicin (CYP inducer), bupropion (CYP2D6 inhibitor and CYP2B6 substrate), ethinyl estradiol/levonorgestrel (CYP3A substrates) and omeprazole (CYP2C19 substrate and inhibitor).



The ratio of central values of the test treatment to the reference treatment for relevant parameters (e.g., area under the plasma concentration-time curve [AUC] and maximum plasma concentration [C max]) was used to assess pharmacokinetic interactions.



Co-administration of vortioxetine had no effect on the AUC or C max of ethinyl estradiol/levonorgestrel or 5'-hydroxyomeprazole, or the AUC of bupropion; the 90 % confidence intervals for these ratios of central values were within 80-125 %. Steady-state AUC and C max of vortioxetine increased when co-administered with bupropion (128 and 114 %, respectively), fluconazole (46 and 15 %, respectively) and ketoconazole (30 and 26 %, respectively), and decreased by 72 and 51 %, respectively, when vortioxetine was co-administered with rifampicin. Concomitant therapy was generally well tolerated; most adverse events were mild or moderate in intensity.



Dosage adjustment may be required when vortioxetine is co-administered with bupropion or rifampicin.
A universal model for mobility and migration patterns

Introduced in its contemporary form in 1946 (ref. 1), but with roots that go back to the eighteenth century, the gravity law is the prevailing framework with which to predict population movement, cargo shipping volume and inter-city phone calls, as well as bilateral trade flows between nations. Despite its widespread use, it relies on adjustable parameters that vary from region to region and suffers from known analytic inconsistencies. Here we introduce a stochastic process capturing local mobility decisions that helps us analytically derive commuting and mobility fluxes that require as input only information on the population distribution. The resulting radiation model predicts mobility patterns in good agreement with mobility and transport patterns observed in a wide range of phenomena, from long-term migration patterns to communication volume between different regions. Given its parameter-free nature, the model can be applied in areas where we lack previous mobility measurements, significantly improving the predictive accuracy of most of the phenomena affected by mobility and transport processes.
Preamputation mirror therapy may prevent development of phantom limb pain: a case series.

We report the cases of 4 patients who performed daily mirror therapy for 2 wk before undergoing elective limb amputation. One patient experienced no phantom limb pain (PLP). Two patients experienced rare episodes of mild PLP without effect on their participation in physical therapy (PT) or their quality of life. One patient reported daily, brief episodes of moderate PLP without effect on his participation in PT or his stated quality of life. These results indicate that preoperative mirror therapy may improve postamputation PT compliance and decrease the incidence of PLP. Future prospective studies are needed to confirm the results of this case series.
Adequacy of food spending is related to housing expenditures among lower-income Canadian households.

A number of studies have pointed to the pressure that housing costs can exert on the resources available for food. The objectives of the present study were to characterise the relationship between the proportion of income absorbed by housing and the adequacy of household food expenditures across the Canadian population and within income quintiles; and to elucidate the impact of receipt of a housing subsidy on adequacy of food expenditures among low-income tenant households.



The 2001 Survey of Household Spending, conducted by Statistics Canada, was a national cross-sectional survey that collected detailed information on expenditures on goods and services. The adequacy of food spending was assessed in relation to the cost of a basic nutritious diet.



Canada.



The person with primary responsibility for financial maintenance from 15 535 households from all provinces and territories.



As the proportion of income allocated to housing increased, food spending adequacy declined significantly among households in the three lowest income quintiles. After accounting for household income and composition, receipt of a housing subsidy was associated with an improvement in adequacy of food spending among low-income tenant households, but still mean food spending fell below the cost of a basic nutritious diet even among subsidised households.



This study indicates that housing costs compromise the food access of some low-income households and speaks to the need to re-examine policies related to housing affordability and income adequacy.
Online Real-Time Multiple Spatiotemporal Action Localisation and Prediction

We present a deep-learning framework for real-time multiple spatio-temporal (S/T) action localisation and classification. Current state-of-the-art approaches work offline, and are too slow to be useful in real-world settings. To overcome their limitations we introduce two major developments. Firstly, we adopt real-time SSD (Single Shot Multi-Box Detector) CNNs to regress and classify detection boxes in each video frame potentially containing an action of interest. Secondly, we design an original and efficient online algorithm to incrementally construct and label ‘action tubes’ from the SSD frame level detections. As a result, our system is not only capable of performing S/T detection in real time, but can also perform early action prediction in an online fashion. We achieve new state-of-the-art results in both S/T action localisation and early action prediction on the challenging UCF101-24 and J-HMDB-21 benchmarks, even when compared to the top offline competitors. To the best of our knowledge, ours is the first real-time (up to 40fps) system able to perform online S/T action localisation on the untrimmed videos of UCF101-24.
Cross site scripting (XSS) attack detection using intrustion detection system

Everyone is now relying on the Internet for our innumerable kind of work; this has increased the opportunity for attackers to corrupt data and make vulnerable. Nowadays diverse kind of attacks is being launched in Cyber Space among which Cross-Site Scripting (Web Application Attack) is amongst top attacks of all time. Proposed work, suggest an outline for a system that can detect Cross-Site Scripting (known as XSS) attack using Intrusion Detection system (IDS). This work focuses on the detection of XSS attack using intrusion detection system. Here attack signature is utilized to detect XSS attack. To test the usefulness and effectiveness of proposed work a proof of concept prototype has been implemented using SNORT IDS. It is observed that proposed system correctly detected XSS attack.
Removal of heavy metals by an Aspergillus terreus strain immobilized in a polyurethane matrix.

The aim was to investigate the biosorption of chromium, nickel and iron from metallurgical effluents, produced by a steel foundry, using a strain of Aspergillus terreus immobilized in polyurethane foam.



A. terreus UFMG-F01 was immobilized in polyurethane foam and subjected to biosorption tests with metallurgical effluents. Maximal metal uptake values of 164.5 mg g(-1) iron, 96.5 mg g(-1) chromium and 19.6 mg g(-1) nickel were attained in a culture medium containing 100% of effluent stream supplemented with 1% of glucose, after 6 d of incubation.



Microbial populations in metal-polluted environments include fungi that have adapted to otherwise toxic concentrations of heavy metals and have become metal resistant. In this work, a strain of A. terreus was successfully used as a metal biosorbent for the treatment of metallurgical effluents.



A. terreus UFMG-F01 was shown to have good biosorption properties with respect to heavy metals. The low cost and simplicity of this technique make its use ideal for the treatment of effluents from steel foundries.
Visual perceptual and handwriting skills in children with Developmental Coordination Disorder.

Children with Developmental Coordination Disorder demonstrate a lack of automaticity in handwriting as measured by pauses during writing. Deficits in visual perception have been proposed in the literature as underlying mechanisms of handwriting difficulties in children with DCD. The aim of this study was to examine whether correlations exist between measures of visual perception and visual motor integration with measures of the handwriting product and process in children with DCD.



The performance of twenty-eight 8-14year-old children who met the DSM-5 criteria for DCD was compared with 28 typically developing (TD) age and gender-matched controls. The children completed the Developmental Test of Visual Motor Integration (VMI) and the Test of Visual Perceptual Skills (TVPS). Group comparisons were made, correlations were conducted between the visual perceptual measures and handwriting measures and the sensitivity and specificity examined.



The DCD group performed below the TD group on the VMI and TVPS. There were no significant correlations between the VMI or TVPS and any of the handwriting measures in the DCD group. In addition, both tests demonstrated low sensitivity.



Clinicians should execute caution in using visual perceptual measures to inform them about handwriting skill in children with DCD.
A Stochastic Collocation Approach to Bayesian Inference in Inverse Problems

We present an efficient numerical strategy for the Bayesian solution of inverse problems. Stochastic collocation methods, based on generalized polynomial chaos (gPC), are used to construct a polynomial approximation of the forward solution over the support of the prior distribution. This approximation then defines a surrogate posterior probability density that can be evaluated repeatedly at minimal computational cost. The ability to simulate a large number of samples from the posterior distribution results in very accurate estimates of the inverse solution and its associated uncertainty. Combined with high accuracy of the gPC-based forward solver, the new algorithm can provide great efficiency in practical applications. A rigorous error analysis of the algorithm is conducted, where we establish convergence of the approximate posterior to the true posterior and obtain an estimate of the convergence rate. It is proved that fast (exponential) convergence of the gPC forward solution yields similarly fast (exponential) convergence of the posterior. The numerical strategy and the predicted convergence rates are then demonstrated on nonlinear inverse problems of varying smoothness and dimension.
An experimental study comparing linguistic phylogenetic reconstruction methods *

The estimation of linguistic evolution has intrigued many researchers for generations, and in just the last few years, several new methods for constructing phylogenies from languages have been produced and used to analyze a number of language families. These analyses have led to a great deal of excitement, both within the field of historical linguistics and in related fields such as archaeology and human genetics. They have also been controversial, since the analyses have not always been consistent with each other, and the differences between different reconstructions have been potentially critical to the claims made by the different groups. In this paper, we report on a simulation study we performed in order to help resolve this controversy, which compares some of the main phylogeny reconstruction methods currently being used in linguistic cladistics. Our simulated datasets varied in the number of contact edges, the degree of parallel evolution and back-mutation (jointly referred to as ‘homoplasy’), the deviation from a lexical clock, and the deviation from the rates-across-sites assumption. We find the accuracy of maximum parsimony, neighbor joining, UPGMA, and the method of Gray & Atkinson, to be remarkably consistent across all the model conditions we studied, with maximum parsimony the best, followed by Gray & Atkinson’s method, then neighbor joining, and finally UPGMA (one of the standard lexicostatistics methods). Furthermore, if linguistic traits (called ‘characters’) are weighted in a maximum parsimony or maximum compatibility analysis, the accuracy of the results depends upon the weighting scheme and the amount of homoplasy in the characters. However, for low homoplasy model conditions and appropriate weighting schemes, weighted parsimony and weighted compatibility generally produce the most accurate results of all methods.
A Deformed-Film UWB Antenna

Recently, microwave ultra-wideband (UWB) technology has attracted much attention in high speed wireless communications, imaging and radar applications. Antennas with very wide impedance bandwidth and stable radiations are required for such systems. Among many UWB antennas, planar types are low profile, light weight, low cost and suitable for mobile devices . However, the planar antennas may not radiate omni-directionally at all operating frequencies because they generally have wide structures and are not rotationally symmetrical. A roll monopole antenna which is constructed by twisting a planar radiator into a roll shape has been proposed for improving radiation characteristics, but the bandwidth of the antenna was limited . In this paper, we will propose a deformed film UWB antenna for operating at the FCC approved UWB of 3.1-10.6 GHz. The antenna is constructed by deforming a planar dipole which has a glass-shaped radiation element . The antenna is optimized for the UWB operation in its planar form and can be deformed by different manners such as folding, meandering or twisting, without much influence on input characteristics. The deformation not only miniaturizes the antenna but also improves its radiation characteristics. To investigate experimentally the antenna, a prototype with a dimension of 20x33 mm is fabricated and then the antenna is deformed by rolling into a circular rod with a diameter of 6.5 mm, or meandering it into a square rod with a cross-sectional dimension of 6x5 mm. It is demonstrated that the deformed antennas still operate at the UWB and have better omni-directional radiation patterns than the antenna in its planar form.
ViSQOL: The Virtual Speech Quality Objective Listener

A model of human speech quality perception has been developed to provide an objective measure for predicting subjective quality assessments. The Virtual Speech Quality  Listener (ViSQOL) model is a signal based full reference metric that uses a spectro-temporal measure of similarity between a reference and a test speech signal. This paper describes the algorithm and compares the results with PESQ for common problems in VoIP: clock drift, associated time warping and jitter. The results indicate that ViSQOL is less prone to underestimation of speech quality in both scenarios than the ITU standard.
Smart Textile Using Hetero-Core Optical Fiber for Heartbeat and Respiration Monitoring

This paper aims to describe a novel smart textile that uses a single-mode hetero-core optical fiber sensor for monitoring heartbeat and respiration. The smart textile was designed by weaving hetero-core optical fibers together with the wool fabric. This novel textile that can detect variations in shapes can be incorporated into clothes. Such clothes can offer comfort to the wearer. To simultaneously monitor heartbeat and respiration, the proposed textile is sewn on to the clothes to be able to sense minute load changes produced by chest movements. The vital signs, which were calculated from the heartbeat and respiration frequency of a healthy adult, while sitting, were in agreement with those verified using commercial monitoring devices. In addition, to confirm the capability of monitoring vital signs, seven monitoring trials were performed in which the subjects were asked to wear and take off the smart cloth. The vital signs rates were successfully extracted within the four beats per minute error by the fiber optic sensor system. The proposed smart textile in clothes can monitor vital signs in daily life activities, such as sitting and standing.
LABORATORY INVESTIGATION OF THROMBOPHILIA

Ph. D. Sandra Margeti} Department of Laboratory Haematology and Coagulation Clinical Institute of Chemistry Medical School University Hospital Sestre milosrdnice Vinogradska 29 10 000 Zagreb, Croatia Tel: +385 1 3787 115 Fax: +385 1 3768 280  Laboratory investigation of thrombophilia is aimed at detecting the well-established hereditary and acquired causes of venous thromboembolism, including activated protein C resistance/factor V Leiden mutation, prothrombin G20210A mutation, deficiencies of the physio logical anticoagulants antithrombin, protein C and protein S, the presence of antiphospholipid antibodies and increased plasma levels of homocysteine and coagulation factor VIII. In contrast, investigation of dysfibrinogenemia, a very rare thrombophilic risk factor, should only be considered in a patient with evidence of familial or recurrent thrombosis in the absence of all evaluated risk factors mentioned above. At this time, thrombophilia investigation is not recommended for other potential hereditary or acquired risk factors whose association with increased risk for thrombosis has not been proven sufficiently to date. In order to ensure clinical relevance of testing and to avoid any misinterpretation of results, laboratory investigation of thrombophilia should always be performed in accordance with the recommended guidelines on testing regarding the careful selection of patients, time of testing and assays and assay methods used. The aim of this review is to summarize the most important aspects on thrombophilia testing, including whom and when to test, what assays and assay methods to use and all other variables that should be considered when performing laboratory investigation of thrombophilia.
Querying Data Services in an Uncertain Environment: A Possibilistic-Based Approach

The acceptance of open data practices by individuals and organizations lead to an enormous explosion in data production on the Internet. The access to a large number of these data is carried out through Web services, which provide a standard way to interact with data. This class of services is known as data services. In this context, users' queries often require the composition of multiple data services to be answered. On the other hand, the data returned by a data service is not always certain due to various raisons, e.g., the service accesses different data sources, privacy constraints, etc. In this paper, we study the basic activities of data services that are affected by the uncertainty of data, more specifically, modeling, invocation and composition. We propose a possibilistic approach that treats the uncertainty in all these activities.
WireCAP: a novel packet capture engine for commodity NICs in high-speed networks

Packet capture is an essential function for many network applications. However, packet drop is a major problem with packet capture in high-speed networks. This paper presents WireCAP, a novel packet capture engine for commodity network interface cards (NICs) in high-speed networks. WireCAP provides lossless zero-copy packet capture and delivery services by exploiting multi-queue NICs and multicore architectures. WireCAP introduces two new mechanisms-the ring-buffer-pool mechanism and the buddy-group-based offloading mechanism-to address the packet drop problem of packet capture in high-speed network. WireCAP is efficient. It also facilitates the design and operation of a user-space packet-processing application. Experiments have demonstrated that WireCAP achieves better packet capture performance when compared to existing packet capture engines.
 In addition, WireCAP implements a packet transmit function that allows captured packets to be forwarded, potentially after the packets are modified or inspected in flight. Therefore, WireCAP can be used to support middlebox-type applications. Thus, at a high level, WireCAP provides a new packet I/O framework for commodity NICs in high-speed networks.