nils-herrmann/clean_scirepeval huggingface dataset:
Measuring and evaluating bitumen coverage of stones using two different digital image analysis methods

The most used pavement for paved roads in the world is asphalt. It is therefore important that the asphalt is as durable as possible to avoid expensive repairs of the roads. One important factor of the durability of the road is the adherence between the stones and the bitumen that holds the stones together. The affinity is tested by the so called rolling bottle test, where one put stones covered in bitumen in a bottle with water and let it roll on a bottle rolling machine. After a while the degree of bitumen coverage is estimated. In this paper, a method to estimate the degree of bitumen coverage using image analysis has been developed instead of the manual estimation that is used today. The presented method works for all colors of the stones and is based on the fact that bitumen reflects light much better than raw stones. A turntable that is rotated somewhat between images is used together with a light source in shape of a quarter of a circle to get as much specular reflections as possible. Then the amount of detected reflections is used to estimate the degree of bitumen coverage. To be able to compare the result with something close to ground truth, the method has been evaluated on lighter stones and compared with a second image analysis method that works well for lighter stones, and the results are promising.
DATA ANALYTICS AND PREDICTIVE ANALYTICS IN THE ERA OF BIG DATA

This chapter outlines the key principles of machine learning and predictive analytics. It explains the new fundamentals of big data and the evolving technology. The chapter follows by the practical advice on how organizations can establish a new culture in order to truly transform their business in the new era. The wave of data frenzy did not happen overnight. Rather, it is a crescendo of events happening since the early 1980s where the fields of business intelligence and predictive analytics were known as 'data mining' a preexisting discipline with another closely related term known as knowledge discovery in databases (KDD) which is the aim of performing data mining. Analytics has a spectrum of methodologies, techniques, and approaches from descriptive, diagnostic, predictive and prescriptive analytics. Most data mining projects today follow the cross industry standard process for data mining (CRISP DM) which was conceived in 1996.
Numerical experience with a derivative free trust funnel method for nonlinear optimization problems with general nonlinear constraints
Venue: Optim. Methods Softw.

A trust funnel method is proposed for solving nonlinear optimization problems with general nonlinear constraints. It extends the one presented by Gould and Toint [Nonlinear programming without a penalty function or a filter.  2010] originally proposed for equality constrained optimization problems only, to problems with both equality and inequality constraints and where simple bounds are also considered. As the original one, our method makes use of neither filter nor penalty functions and considers the objective function and the constraints as independently as possible. To handle the bounds, an active set approach is employed. We then exploit techniques developed for derivative free optimization (DFO) to obtain a method that can also be used to solve problems where the derivatives are unavailable or are available at a prohibitive cost. The resulting approach extends the DEFT FUNNEL algorithm presented by Sampaio and Toint [A derivative free trust funnel method for equality constrained nonlinear optimization.  2015] which implements a derivative free trust funnel method for equality constrained problems. Numerical experiments with the extended algorithm show that our approach compares favourably to other well known model based algorithms for DFO.
A projected gradient method for optimization over density matrices
Venue: Optim. Methods Softw.

An ensemble of quantum states can be described by a Hermitian, positive semidefinite and unit trace matrix called density matrix. Thus, the study of methods for optimizing a certain function (energy, entropy) over the set of density matrices has a direct application to important problems in quantum information and computation. We propose a projected gradient method for solving such problems. By exploiting the geometry of the feasible set, which is the intersection of the cone of Hermitian positive semidefinite matrices with the hyperplane defined by the unit trace constraint, we describe an efficient procedure to compute the projection onto this set using the Frobenius norm. Some important applications, such as quantum state tomography, are described and numerical experiments illustrate the effectiveness of the method when compared to previous methods based on fixed point iterations or semidefinite programming.
A second order method for convex 1 regularized optimization with active set prediction
Venue: Optim. Methods Softw.

We describe an active set method for the minimization of an objective function ph that is the sum of a smooth convex function f and an regularization term. A distinctive feature of the method is the way in which active set identification and second order subspace minimization steps are integrated to combine the predictive power of the two approaches. At every iteration, the algorithm selects a candidate set of free and fixed variables, performs an (inexact) subspace phase, and then assesses the quality of the new active set. If it is not judged to be acceptable, then the set of free variables is restricted and a new active set prediction is made. We establish global convergence for our approach under the assumptions of Lipschitz continuity and strong convexity of f, and compare the new method against state of the art codes.
Community detection using meta heuristic approach: Bat algorithm variants
Venue: 2016 Ninth International Conference on Contemporary Computing (IC3)

In the present world, it is hard to overlook the omnipresence of 'network' Be it the study of internet structure, mobile network, protein interactions or social networks, they all religiously emphasizes on network and graph studies. Social network analysis is an emerging field including community detection as its key task. A community in a network, depicts group of nodes in which density of links is high. To find the community structure modularity metric of social network has been used in different optimization approaches like greedy optimization, simulated annealing, extremal optimization, particle swarm optimization and genetic approach. In this paper we have not only introduced modularity metrics but also hamiltonian function (potts model) amalgamated with meta heuristic optimization approaches of Bat algorithm and Novel Bat algorithm. By utilizing objective functions (modularity and hamiltonian) with modified discrete version of Bat and Novel Bat algorithm we have devised four new variants for community detection. The results obtained across four variants are compared with traditional approaches like Girvan and Newman, fast greedy modularity optimization, Reichardt and Bornholdt, Ronhovde and Nussinov, and spectral clustering. After analyzing the results, we have dwelled upon a promising outcome supporting the modified variants.
Wearable Medical Monitoring Systems Based on Wireless Networks: A Review
Venue: IEEE Sensors Journal

The last decade has witnessed a rapid increase of interest in new sensing and monitoring devices, including wireless wearable mobile devices and sensing networks for medical health applications. This paper reviews current wearable mobile medical monitoring systems (WMMMSs) with emphasis on devices based on textile and wireless sensing networks. These monitoring systems consist of various types of small physiological sensors, transmission modules, and processing capabilities. In addition, WMMMSs have a potential to change the health care model by providing inexpensive wearable unobtrusive solutions for continuous medical health monitoring. It is with the hope that the current survey is able to provide a direction for future research improvements and also serve as a reference for current achievements and their maturity level. In this review, a great number of system implementations are compared according to different classifications. Besides, these systems also act as an effective approach to identify the technological advantages and disadvantages of the current state of the art in wearable devices solutions.
Strategic Workforce Planning for Health Human Resources
Venue: The Canadian journal of nursing research Revue canadienne de recherche en sciences infirmieres

Health care organizations provide services in a challenging environment, making the introduction of health human resources initiatives especially critical for safe patient care.  To demonstrate how one specialty hospital in Ontario, Canada, leveraged an employment policy to stabilize its nursing workforce over a six year period (2007 to 2012)  An observational cross sectional study was conducted in which administrative data were analyzed to compare full time status and retention of new nurses prepolicy and during the policy. The Professionalism and Environmental Factors in the Workplace Questionnaire(r) was used to compare new nurses hired into the study hospital with new nurses hired in other health care settings.  There was a significant increase in full time employment and a decrease in part time employment in the study hospital nursing workforce. On average, 26% of prepolicy new hires left the study hospital within one year of employment compared to 5% of new hires during policy implementation. The hospital nurses scored significantly higher than nurses employed in other health care settings on 5 out of 13 subscales of professionalism.  Decision makers can use these findings to develop comprehensive health human resources guidelines and mechanisms that support strategic workforce planning to sustain and strengthen the health care system.
A Hybrid Clustering Technique Combining A PSO Algorithm with K Means

Particle Swarm Optimization (PSO) is an evolutionary computation technique. Separate adjustment to inertia weight and learning factors in PSO undermines the integrity and intelligent characteristic in the evolutionary process of particle swarm to some extent, thus it is not suitable for solving most complicated optimization problems. On the basis of previous researches, the aim of this study was to improve the computational efficiency of PSO and avoid premature convergence for multimodal, higher dimensional complicated optimization problems by considering the mutual influences of inertia weight and learning factors on the updates of particle's velocities. A typical data analytical scenario is a multidimensional problem and data clustering can lead to multi spatial analysis. Cluster can be a result of various algorithms. In this paper PSO based k means clustering is applied to generate clusters. And provide multimodal and higher dimensional complicated optimization problems, and can accelerate convergence speed, improve optimization quality effectively in comparison to the algorithms of PSO Kmeans.
What do urologists think patients need to know when starting on androgen deprivation therapy? The perspective from Canada versus countries with lower gross domestic product
Venue: Translational andrology and urology

Androgen deprivation therapy (ADT) side effects are numerous and negatively impact prostate cancer patients' quality of life. There is considerable discrepancy though among Canadian urologists regarding what ADT side effects and side effect management strategies. Little is known about global differences in ADT patient education.  International respondents were recruited via online posting and at an international urology conference. Hypotheses suggest that economic and cultural differences influence patient education practices; therefore, international respondents were divided into 3 categories (high, medium, and low gross domestic product)  No differences were found between responses from Canadian urologists and high GDP countries. Compared to responses from low GDP countries, Canadian urologists are more likely to endorse informing patients about: osteoporosis, loss of muscle mass, weight gain, fatigue/sleep disturbance, relationship changes, cognitive changes, and loss of body hair. Infertility was the only side effect more often disclosed by urologists in low GDP counties. Recommended management strategies for hot flashes are more likely to be pharmaceutical in Canada, and behavioral in low GDP countries. Management strategies for gynecomastia are emphasized more in low GDP countries. Physical exercise is endorsed consistently more often by Canadian urologists.  ADT educational practices vary greatly between Canada and lower GDP countries. Factors that could contribute to differences include economics (e.g. ADT drug costs) differences in side effect presentation due to different ADT drugs used, racial differences in perceived side effect burden, disease status at ADT commencement, and cultural differences in patient physician shared decision making.
Alleviation of cadmium stress in Solanum lycopersicum L. by arbuscular mycorrhizal fungi via induction of acquired systemic tolerance
Venue: Saudi journal of biological sciences

Experiments were conducted to evaluate cadmium (Cd) stress induced changes in growth, antioxidants and lipid composition of Solanum lycopersicum with and without arbuscular mycorrhizal fungi (AMF) Cadmium stress (50 mM) caused significant changes in the growth and physio biochemical attributes studied. AMF mitigated the deleterious impact of Cd on the parameters studied. Cadmium stress increased malonaldehyde and hydrogen peroxide production but AMF reduced these parameters by mitigating oxidative stress. The activity of antioxidant enzymes enhanced under Cd treatment and AMF inoculation further enhanced their activity, thus strengthening the plant's defense system. Proline and phenol content increased in Cd treated as well as AMF inoculated plants providing efficient protection against Cd stress. Cadmium treatment resulted in great alterations in the main lipid classes leading to a marked change in their composition. Cadmium stress caused a significant reduction in polyunsaturated fatty acids resulting in enhanced membrane leakage. The present study supports the use of AMF as a biological means to ameliorate Cd stress induced changes in tomato.
Prevalence of Trypanosoma cruzi's Discrete Typing Units in a cohort of Latin American migrants in Spain.
Venue: Acta tropica

Chagas disease is caused by the protozoan Trypanosoma cruzi. This is an endemic disease in the Americas, but increased migration to Europe has made it emerge in countries where it was previously unknown, being Spain the second non endemic country in number of patients. T. cruzi is a parasite with a wide genetic diversity, which has been grouped by consensus into 6 Discrete Typing Units (DTUs) affecting humans. Some authors have linked these DTUs either to a specific epidemiological context or to the different clinical presentations. Our main objective was to describe the T. cruzi DTUs identified from a population of chronically infected Latin American migrants attending a reference clinic in Madrid. 149 patients meeting this condition were selected for the study. Molecular characterization was performed by an algorithm that combines PCR of the intergenic region of the mini exon gene, the 24Sa and 18S regions of rDNA and the variable region of the satellite DNA. A descriptive analysis was performed and associations between geographical/clinical data and the different DTUs were tested. DTUs could be determined in 105 out of 149 patients, 93.3% were from Bolivia, 67.7% were women and median age was 35 years (IQR 29 44) The most common DTU found was TcV (58; 55.2% followed by TcIV (17; 16.2% TcII (10; 9.5% and TcI (4; 3.8% TcIII and TcVI were not identified from any patient, and 15.2% patients presented mixed infections. In addition, we determined DTUs after treatment in a subset of patients. In 57% patients had different DTUs before and after treatment. DTUs distribution from this study indicates active transmission of T. cruzi is occurring in Bolivia, in both domestic and sylvatic cycles. TcIV was confirmed as a cause of chronic human disease. The current results indicate no correlation between DTU and any specific clinical presentation associated with Chagas disease, nor with geographical origin. Treatment with benznidazole does not always clear T. cruzi's genetic material from blood, and DTUs detected in the same patient may vary over time indicating that polyparasitism is frequent.
Screening North American plant extracts in vitro against Trypanosoma brucei for discovery of new antitrypanosomal drug leads
Venue: BMC Complementary and Alternative Medicine

BackgroundHuman African Trypanosomiasis (HAT) is a protozoan parasitic disease caused by Trypanosoma brucei. The disease is endemic in regions of sub Saharan Africa, covering 36 countries and more than 60 million people at the risk. Only few drugs are available for the treatment of HAT. Current drugs suffer from severe toxicities and require intramuscular or intravenous administrations. The situation is further aggravated due to the emergence of drug resistance. There is an urgent need of new drugs that are effective orally against both stages of HAT. Natural products offer an unmatched source for bioactive molecules with new chemotypes.MethodsThe extracts prepared from 522 plants collected from various parts of the North America were screened in vitro against blood stage trypamastigote forms of T. brucei. Active extracts were further screened at concentrations ranging from 10 to 0.4 mg/mL. Active extracts were also investigated for toxicity in Differentiated THP1 cells at 10 mg/mL concentration. The results were computed for dose response analysis and determination of IC50/IC90 values. significant number (150) of extracts showed >90 inhibition of growth of trypomastigote blood forms of T. brucei in primary screening at 20 mg/mL concentration. The active extracts were further investigated for dose response inhibition of T. brucei growth. The antitrypansomal activity of 125 plant extracts was confirmed with IC50 10 mg/mL. None of these active extracts showed toxicity against differentiated THP1 cells. Eight plants extracts namely, Alnus rubra, Hoita macrostachya, Sabal minor, Syzygium aqueum, Hamamelis virginiana, Coccoloba pubescens, Rhus integrifolia and Nuphar luteum were identified as highly potent antitrypanosomal extracts with IC50 values <1 mg/mL.ConclusionsLimited phytochemical and pharmacological reports are available for the lead plant extracts with potent antitrypanosomal activity. Follow up evaluation of these plant extracts is likely to yield new antitrypanosomal drug leads or alternate medicines for treatment of HAT.
Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge
Venue: Front. Microbiol.

To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35degN; 29degW) In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro X ray Absorption Near Edge Structure at the Fe K edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron oxides trapped in a palagonite like structure with thicknesses up to 150 mm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron oxidizer Mariprofundus ferrooxydans PV 1. Conversely, the oxidized basaltic glass showed the absence of iron oxides enriched surface deposits and correspondingly there was a lack of known iron oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron oxidizing M. ferrooxydans DIS 1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.
Agglutination of benthic foraminifera in relation to mesoscale bathymetric features in the abyssal NE Atlantic (Porcupine Abyssal Plain)

Abyssal hills, small topographic features rising above the abyssal seafloor 1000 m altitude) have distinct environmental characteristics compared to abyssal plains, notably the presence of coarser grained sediments. As a result, they are a major source of habitat heterogeneity in the deep sea. The aim of this study was to investigate whether there is a link between abyssal hills and the test characteristics of selected agglutinated benthic foraminiferal species. We analysed 1) the overall morphometry, and 2) the granulometric and chemical (elemental) characteristics of the agglutinated tests of ten common foraminiferal species (Adercotryma glomerata, Ammobaculites agglutinans, Cribrostomoides subglobosus, Lagenammina sp.1, Nodulina dentaliniformis, Portatrochammina murrayi, three Reophax sp. and Recurvoides sp. 9) at four sites (two on top of abyssal hills and two on the adjacent plain) in the area of the Porcupine Abyssal Plain Sustained Observatory, northeast Atlantic. The foraminiferal test data were compared with the particle size distribution and elemental composition of sediments from the study sites in order to explore possible grain size and mineral selectivity. We found differences in the visual appearance of the tests (i.e. the degree of irregularity in their shape) which was confirmed by morphometric analyses, related to seafloor topography. The agglutinated foraminifera selected different sized particles on hills and plains, reflecting the distinct granulometric characteristics of these settings. These characteristics (incorporation of coarse particles, test morphometry) could provide evidence for the recognition of ancient abyssal hill environments, as well as other palaeoceanographic settings that were characterised by enhanced current flow. Furthermore, analyses of sediment samples from the hill and plain sites using wavelength dispersive X ray fluorescence (WD XRF) yielded different elemental profiles from the plains, probably a result of winnowing on the hills, although all samples were carbonate rich. In contrast, the majority of the agglutinated tests were rich in silica, suggesting a preferential selection for quartz.