nils-herrmann/clean_scirepeval huggingface dataset:
An ant colony system empowered variable neighborhood search algorithm for the vehicle routing problem with simultaneous pickup and delivery
Venue: Expert Syst. Appl.

The Vehicle Routing Problem with Simultaneous Pickup and Delivery is considered.A hybrid algorithm that combines ACS and VNS approach is developed.A number of well known benchmark problems are solved and compared.Proposed algorithm outperformed perturbation based VNS and local search based ACS.Some new best solutions for benchmark problem instances are found. Along with the progress in computer hardware architecture and computational power, in order to overcome technological bottlenecks, software applications that make use of expert and intelligent systems must race against time where nanoseconds matter in the long awaited future. This is possible with the integration of excellent solvers to software engineering methodologies that provide optimization based decision support for planning. Since the logistics market is growing rapidly, the optimization of routing systems is of primary concern that motivates the use of vehicle routing problem (VRP) solvers as software components integrated as an optimization engine. A critical success factor of routing optimization is quality vs. response time performance. Less time consuming and more efficient automated processes can be achieved by employing stronger solution algorithms. This study aims to solve the Vehicle Routing Problem with Simultaneous Pickup and Delivery (VRPSPD) which is a popular extension of the basic Vehicle Routing Problem arising in real world applications where pickup and delivery operations are simultaneously taken into account to satisfy the vehicle capacity constraint with the objective of total travelled distance minimization. Since the problem is known to be NP hard, a hybrid metaheuristic algorithm based on an ant colony system (ACS) and a variable neighborhood search (VNS) is developed for its solution. VNS is a powerful optimization algorithm that provides intensive local search. However, it lacks a memory structure. This weakness can be minimized by utilizing long term memory structure of ACS and hence the overall performance of the algorithm can be boosted. In the proposed algorithm, instead of ants, VNS releases pheromones on the edges while ants provide a perturbation mechanism for the integrated algorithm using the pheromone information in order to explore search space further and jump from local optima. The performance of the proposed ACS empowered VNS algorithm is studied on well known benchmarks test problems taken from the open literature of VRPSPD for comparison purposes. Numerical results confirm that the developed approach is robust and very efficient in terms of both solution quality and CPU time since better results provided in a shorter time on benchmark data sets is a good performance indicator.
Occurrence of Giardia intestinalis and Cryptosporidium sp. in wastewater samples from Sao Paulo State, Brazil, and Lima, Peru
Venue: Environmental Science and Pollution Research

The objectives of the study were to detect and genotype Cryptosporidium spp. and Giardia intestinalis in wastewater samples obtained from five cities with high transit of people in the State of Sao Paulo, Brazil, and at the entrance of a Wastewater Treatment Plant (WWTP) in Lima, Peru. Samples were collected and concentrated by centrifugation. The genomic DNA was extracted for molecular characterization by nested PCR for Cryptosporidium and double nested PCR for Giardia, followed by sequencing and phylogenetic analysis. G. intestinalis was found in 63.6 of the samples, and the human assemblages A and B were identified. Cryptosporidium sp. was found in 36.4 of the samples, and the species were corresponding to Cryptosporidium hominis, Cryptosporidium cuniculus, and Cryptosporidium muris. Results revealed the presence of human pathogenic Cryptosporidium species and G. intestinalis human pathogenic assemblages. Molecular tools highlight the importance to map the genetic diversity of these parasites, as well as to detect their epidemiological circulation pathway in the environment.
SVM Prot 2016: A Web Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity
Venue: PloS one

Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM Prot web server employed a machine learning method for predicting protein functional families from protein sequences irrespective of similarity, which complemented those similarity based and other methods in predicting diverse classes of proteins including the distantly related proteins and homologous proteins of different functions. Since its publication in 2003, we made major improvements to SVM Prot with (1) expanded coverage from 54 to 192 functional families, (2) more diverse protein descriptors protein representation, (3) improved predictive performances due to the use of more enriched training datasets and more variety of protein descriptors, (4) newly integrated BLAST analysis option for assessing proteins in the SVM Prot predicted functional families that were similar in sequence to a query protein, and (5) newly added batch submission option for supporting the classification of multiple proteins. Moreover, 2 more machine learning approaches, K nearest neighbor and probabilistic neural networks, were added for facilitating collective assessment of protein functions by multiple methods. SVM Prot can be accessed at http:/bidd2.nus.edu.sg/cgi bin/svmprot/svmprot.cgi.
Solving Constraint Satisfaction Problems with Networks of Spiking Neurons
Venue: Front. Neurosci.

Network of neurons in the brain apply unlike processors in our current generation of computer hardware an event based processing strategy, where short pulses (spikes) are emitted sparsely by neurons to signal the occurrence of an event at a particular point in time. Such spike based computations promise to be substantially more power efficient than traditional clocked processing schemes. However, it turns out to be surprisingly difficult to design networks of spiking neurons that can solve difficult computational problems on the level of single spikes, rather than rates of spikes. We present here a new method for designing networks of spiking neurons via an energy function. Furthermore, we show how the energy function of a network of stochastically firing neurons can be shaped in a transparent manner by composing the networks of simple stereotypical network motifs. We show that this design approach enables networks of spiking neurons to produce approximate solutions to difficult (NP hard) constraint satisfaction problems from the domains of planning/optimization and verification/logical inference. The resulting networks employ noise as a computational resource. Nevertheless, the timing of spikes plays an essential role in their computations. Furthermore, networks of spiking neurons carry out for the Traveling Salesman Problem a more efficient stochastic search for good solutions compared with stochastic artificial neural networks (Boltzmann machines) and Gibbs sampling.
Constraint satisfaction problems for reducts of homogeneous graphs
Venue: ICALP

For $n\geq 3$ let (H_n, E) denote the $n$ th Henson graph, i.e. the unique countable homogeneous graph with exactly those finite graphs as induced subgraphs that do not embed the complete graph on $n$ vertices. We show that for all structures \Gamma$ with domain $H_n$ whose relations are first order definable in (H_n,E) the constraint satisfaction problem for \Gamma$ is either in P or is NP complete. We moreover show a similar complexity dichotomy for all structures whose relations are first order definable in a homogeneous graph whose reflexive closure is an equivalence relation. Together with earlier results, in particular for the random graph, this completes the complexity classification of constraint satisfaction problems of structures first order definable in countably infinite homogeneous graphs: all such problems are either in P or NP complete.
The algebraic dichotomy conjecture for infinite domain Constraint Satisfaction Problems
Venue: 2016 31st Annual ACM/IEEE Symposium on Logic in Computer Science (LICS)

We prove that an o categorical core structure primitively positively interprets all finite structures with parameters if and only if some stabilizer of its polymorphism clone has a homomorphism to the clone of projections, and that this happens if and only if its polymorphism clone does not contain operations a,b, s satisfying the identity as(x, y, x, z, y, z) bs(y, x, z, x, z, y).This establishes an algebraic criterion equivalent to the conjectured borderline between P and NP complete CSPs over reducts of finitely bounded homogenous structures, and accomplishes one of the steps of a proposed strategy for reducing the infinite domain CSP dichotomy conjecture to the finite case.Our theorem is also of independent mathematical interest, characterizing a topological property of any o categorical core structure (the existence of a continuous homomorphism of a stabilizer of its polymorphism clone to the projections) in purely algebraic terms (the failure of an identity as above)
3D robotic welding with a laser profile scanner
Venue: 2016 International Conference on Control, Automation and Information Sciences (ICCAIS)

This paper describes the design and development of a cognitive module for 3D robotic welding using TIG or laser technology. This area is constantly evolving with the needs to solve complex problems of welding automatization and robotization, and also thanks to the continuous advances in measurement technology and robotics. Besides the use of welding robots for serial production with dedicated tightly defined trajectories, systems for automatic welding of a previously undefined path or paths, which the operator can't manually define because of its complexity, are developed. This paper covers the general description of the cognitive module and its required functions. After that, the procedure for 3D robotic welding with a laser profile scanner is described in more detail. The task of controlling the end effector of the robot during the welding process is described. Then an algorithm for 3D model construction based on data from the profile scanner is presented. Development of the cognitive module prototype with use of a 2D profile scanner led to experimental evaluation of its function in the task of automatic cavity repair, which is discussed in the last part of the paper.
Estrogens and selective estrogen receptor modulators in acromegaly
Venue: Endocrine

Despite recent advances in acromegaly treatment by surgery, drugs, and radiotherapy, hormonal control is still not achieved by some patients. The impairment of IGF 1 generation by estrogens in growth hormone deficient patients is well known. Patients on oral estrogens need higher growth hormone doses in order to achieve normal IGF 1 values. In the past, estrogens were one of the first drugs used to treat acromegaly. Nevertheless, due to the high doses used and the obvious side effects in male patients, this strategy was sidelined with the development of more specific drugs, as somatostatin receptor ligands and dopamine agonists. In the last 15 years, the antagonist of growth hormone receptor became available, making possible IGF 1 control of the majority of patients on this particular drug. However, due to its high cost, pegvisomant is still not available in many centers around the world. In this setting, the effect of estrogens and also of selective estrogen receptor modulators on IGF 1 control was reviewed, and proved to be an ancillary tool in the management of acromegaly. This review describes data concerning their efficacy and place in the treatment algorithm of acromegaly.
Genetic Predictors of Response to Different Medical Therapies in Acromegaly.
Venue: Progress in molecular biology and translational science

In the era of predictive medicine, management of diseases is evolving into a more personal and individualized approach, as more data are available regarding clinical, biochemical, radiological, molecular, histopathological, and genetic aspects. In the particular setting of acromegaly, which is a rare, chronic, debilitating, and disfiguring disease, an optimized approach deems even more necessary, especially because of an associated increased morbidity and mortality, the impact on patients' quality of life, and the increased cost of frequently necessary life long treatments. In this paper, we review the available studies that address potential genetic influences on acromegaly, their role in the outcome, and response to treatments, as well as their contribution to the risk of developing side effects. We focus mainly on pharmacogenetic factors involved during treatment with dopamine agonists, somatostatin analogs, and pegvisomant. Specifically, mutations in dopamine receptors, somatostatin receptors, growth hormone receptors, and metabolic pathways involved in growth hormone action; polymorphisms in the insulin like growth factor and the insulin like growth factor binding proteins; and polymorphisms in other genes that may determine differences in the frequency of developing adverse events.
Update on the use of oral octreotide therapy for acromegaly
Venue: Expert review of endocrinology metabolism

Somatostatin analogs are most commonly used in pharmacological treatment of acromegaly. Pegvisomant and dopamine agonists are alternatives, which are used to a lesser extent. Dopamine agonists are the only orally applicable medication but are less effective than the other options. For a large number of patients, life long pharmacotherapy has to be applied and frequent injections represent a reduction of quality of life for many of them.  Recently published evidence for the use of oral octreotide therapy for acromegaly.  Oral octreotide is a novel and effective treatment for acromegaly and the side effects have been shown to be comparable to the injectable SSAs. The combination with a transient permeability enhancer allows intestinal permeation but also enables molecules with a size <70 kDa to pass transiently. This does not seem to have an acute or subacute consequence, but the long term effect is still elusive. Therefore, more long term trials are desirable.
BMI and all cause mortality: systematic review and non linear dose response meta analysis of 230 cohort studies with 3.74 million deaths among 30.3 million participants
Venue: British Medical Journal

To conduct a systematic review and meta analysis of cohort studies of body mass index (BMI) and the risk of all cause mortality, and to clarify the shape and the nadir of the dose response curve, and the influence on the results of confounding from smoking, weight loss associated with disease, and preclinical disease. Data sources PubMed and Embase databases searched up to 23 September 2015. Study selection Cohort studies that reported adjusted risk estimates for at least three categories of BMI in relation to all cause mortality.  Summary relative risks were calculated with random effects models. Non linear associations were explored with fractional polynomial models.  230 cohort studies (207 publications) were included. The analysis of never smokers included 53 cohort studies (44 risk estimates) with >738 144 deaths and >9 976 077 participants. The analysis of all participants included 228 cohort studies (198 risk estimates) with >3 744 722 deaths among 30 233 329 participants. The summary relative risk for a 5 unit increment in BMI was 1.18 (95% confidence interval 1.15 to 1.21; I2=95% n=44) among never smokers, 1.21 (1.18 to 1.25; I2=93% n=25) among healthy never smokers, 1.27 (1.21 to 1.33; I2=89% n=11) among healthy never smokers with exclusion of early follow up, and 1.05 (1.04 to 1.07; I2=97% n=198) among all participants. There was a J shaped dose response relation in never smokers (Pnon linearity <0.001) and the lowest risk was observed at BMI 23 24 in never smokers, 22 23 in healthy never smokers, and 20 22 in studies of never smokers with =20 years' follow up. In contrast there was a U shaped association between BMI and mortality in analyses with a greater potential for bias including all participants, current, former, or ever smokers, and in studies with a short duration of follow up <5 years or <10 years) or with moderate study quality scores.  Overweight and obesity is associated with increased risk of all cause mortality and the nadir of the curve was observed at BMI 23 24 among never smokers, 22 23 among healthy never smokers, and 20 22 with longer durations of follow up. The increased risk of mortality observed in underweight people could at least partly be caused by residual confounding from prediagnostic disease. Lack of exclusion of ever smokers, people with prevalent and preclinical disease, and early follow up could bias the results towards a more U shaped association.
The Heart of 25 by 25: Achieving the Goal of Reducing Global and Regional Premature Deaths From Cardiovascular Diseases and Stroke: A Modeling Study From the American Heart Association and World Heart Federation.
Venue: Global heart

In 2011, the United Nations set key targets to reach by 2025 to reduce the risk of premature noncommunicable disease death by 25% by 2025. With cardiovascular disease being the largest contributor to global mortality, accounting for nearly half of the 36 million annual noncommunicable disease deaths, achieving the 2025 goal requires that cardiovascular disease and its risk factors be aggressively addressed. The Global Cardiovascular Disease Taskforce, comprising the World Heart Federation, American Heart Association, American College of Cardiology Foundation, European Heart Network, and European Society of Cardiology, with expanded representation from Asia, Africa, and Latin America, along with global cardiovascular disease experts, disseminates information and approaches to reach the United Nations 2025 targets. The writing committee, which reflects Global Cardiovascular Disease Taskforce membership, engaged the Institute for Health Metrics and Evaluation, University of Washington, to develop region specific estimates of premature cardiovascular mortality in 2025 based on various scenarios. Results show that >5 million premature CVD deaths among men and 2.8 million among women are projected worldwide by 2025, which can be reduced to 3.5 million and 2.2 million, respectively, if risk factor targets for blood pressure, tobacco use, diabetes mellitus, and obesity are achieved. However, global risk factor targets have various effects, depending on region. For most regions, United Nations targets for reducing systolic blood pressure and tobacco use have more substantial effects on future scenarios compared with maintaining current levels of body mass index and fasting plasma glucose. However, preventing increases in body mass index has the largest effect in some high income countries. An approach achieving reductions in multiple risk factors has the largest impact for almost all regions. Achieving these goals can be accomplished only if countries set priorities, implement cost effective population wide strategies, and collaborate in public private partnerships across multiple sectors.
Wave induced dynamics of flexible blades

In this paper, we present an experimental and numerical study that describes the motion of flexible blades, scaled to be dynamically similar to natural aquatic vegetation, forced by wave induced oscillatory flows. For the conditions tested, blade motion is governed primarily by two dimensionless variables: (i) the Cauchy number, Ca, which represents the ratio of the hydrodynamic forcing to the restoring force due to blade stiffness, and (ii) the ratio of the blade length to the wave orbital excursion, L. For flexible blades with Ca 1 the relationship between drag and velocity can be described by two different scaling laws at the large and small excursion limits. For large excursions L 1 the flow resembles a unidirectional current and the scaling laws developed for steady flow reconfiguration studies hold. For small excursions L 1 the beam equations may be linearized and a different scaling law for drag applies. The experimental force measurements suggest that the small excursion scaling applies even for intermediate cases with L O 1 The numerical model employs the well known Morison force formulation, and adequately reproduces the observed blade dynamics and measured hydrodynamic forces without the use of any fitted parameters. For Ca 1 the movement of the flexible blades reduces the measured and modeled hydrodynamic drag relative to a rigid blade of the same morphology. However, in some cases with Ca O 1 the measured hydrodynamic forces generated by the flexible blades exceed those generated by rigid blades, but this is not reproduced in the model. Observations of blade motion suggest that this unusual behavior is related to an unsteady vortex shedding event, which the simple numerical model cannot reproduce. Finally, we also discuss implications for the modeling of wave energy dissipation over canopies of natural aquatic vegetation.
State of the art in the aeroelasticity of wind turbine blades: aeroelastic modelling

With the continuous increasing size and flexibility of large wind turbine blades, aeroelasticity has been becoming a significant subject for wind turbine blade design. There have been some examples of commercially developed wind turbines experiencing aeroelastic instability problems in the last decade, which spokes for the necessity of aeroelastic modelling of wind turbine blades. This paper presents the state of the art aeroelastic modelling of wind turbine blades, provides a comprehensive review on the available models for aerodynamic, structural and cross sectional analysis, discusses the advantages and disadvantages of these models, and outlines the current implementations in this field. This paper is written for both researchers new to this research field by summarising underlying theory whilst presenting a comprehensive review on the latest studies, and experts in this research field by providing a comprehensive list of relevant references in which the details of modelling approaches can be obtained.
Damage and nonlinearities detection in wind turbine blades based on strain field pattern recognition. FBGs, OBR and strain gauges comparison

A 13.5 m wind turbine blade prototype was designed and made of glass fiber and vinylester resin doped with carbon nanofibers. The blade was manufactured using Light RTM (Resin Transfer Molding) as a monocoque structure with a PVC foam core. Within the presented work, a methodology for instrumenting the blade with Fiber Optic Sensors (FOS) embedded into the structure during the manufacturing process was developed. Two different FOS technologies for strain sensing were embedded into the blade: Fiber Bragg Gratings (FBGs) and a plain fiber optic for distributed sensing using an Optical Backscatter Reflectometer (OBR) Besides the FOS, traditional electrical extensometers were bonded to the surface of the blade. By using Hierarchical nonlinear principal component analysis (h NLPCA) it was possible to perform a pattern recognition technique based on the strain field inferred from the measurements acquired by different sensors. Defects and nonlinearities could be detected during the certification testing of the blades, avoiding the premature failure of the structure. Several static tests were conducted, including a test campaign with known artificial damages induced into the structure and the sensitivity of the technique was evaluated. The results showed that every damages could be detected by using different sensing techniques.