nils-herrmann/clean_scirepeval huggingface dataset:
Titanium dioxide in our everyday life; is it safe?

Titanium dioxide (TiO(2)) is considered as an inert and safe material and has been used in many applications for decades. However, with the development of nanotechnologies TiO(2) nanoparticles, with numerous novel and useful properties, are increasingly manufactured and used. Therefore increased human and environmental exposure can be expected, which has put TiO(2) nanoparticles under toxicological scrutiny. Mechanistic toxicological studies show that TiO(2) nanoparticles predominantly cause adverse effects via induction of oxidative stress resulting in cell damage, genotoxicity, inflammation, immune response etc. The extent and type of damage strongly depends on physical and chemical characteristics of TiO(2) nanoparticles, which govern their bioavailability and reactivity. Based on the experimental evidence from animal inhalation studies TiO(2) nanoparticles are classified as "possible carcinogenic to humans" by the International Agency for Research on Cancer and as occupational carcinogen by the National Institute for Occupational Safety and Health. The studies on dermal exposure to TiO(2) nanoparticles, which is in humans substantial through the use of sunscreens, generally indicate negligible transdermal penetration; however data are needed on long-term exposure and potential adverse effects of photo-oxidation products. Although TiO(2) is permitted as an additive (E171) in food and pharmaceutical products we do not have reliable data on its absorption, distribution, excretion and toxicity on oral exposure. TiO(2) may also enter environment, and while it exerts low acute toxicity to aquatic organisms, upon long-term exposure it induces a range of sub-lethal effects.



Until relevant toxicological and human exposure data that would enable reliable risk assessment are obtained, TiO(2) nanoparticles should be used with great care.
An improved general amino acid replacement matrix.

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG.
Reinforcement learning for quality of service in mobile ad hoc network (MANET)

It is very difficult to find feasible QoS (Quality of service) routes in the mobile ad hoc networks (MANETs), because of the nature constrains of it, such as dynamic network topology, wireless communication link and limited process capability of nodes. In order to reduce average cost in flooding path discovery scheme of the traditional MANETs routing protocols and increase the probability of success in finding QoS feasible paths and It proposed a heuristic and distributed route discovery new method supports QoS requirement for MANETs in this study. This method integrates a distributed route discovery scheme with a Reinforcement Learning (RL) method that only utilizes the local information for the dynamic network environment; and the route expand scheme based on Cluster based Routing Algorithms (CRA) method to find more new feasible paths and avoid the problem of optimize timing in previous smart net Quality of service in MANET. In this paper proposed method Compared with traditional method, the experiment results shoItd the network performance is improved optimize timing, efficient and effective.
Data Correction for Gantry-tilted Local CT

Gantry-tilted helical multi-slice computed tomography (CT) refers to the helical scanning CT system equipped with multi-row detector operating at some gantry tilting angle. Its purpose is to avoid the area which is vulnerable to the X-ray radiation. The local tomography is to reduce the total radiation dose by only scanning the region of interest for image reconstruction. In this paper we consider the scanning scheme, and incorporate the local tomography technique with the gantry-tilted helical multi-slice CT. The image degradation problem caused by gantry tilting is studied, and a new error correction method is proposed to deal with this problem in the local CT. Computer simulation shows that the proposed method can enhance the local imaging performance in terms of image sharpness and artifacts reduction
Control Software Synthesis and Validation for a Vehicular Electric Power Distribution Testbed

Modern aircraft increasingly rely on electric power, resulting in high safety criticality and complexity in their electric powergenerationanddistribution systems.Motivatedby the resulting rapid increase in the costs andduration of the design cycles for such systems, the use of formal specification and automated correct-by-construction control protocols synthesis for primarydistribution in vehicular electric power networks is investigated.Adesignworkflow is discussed that aims to transition from the traditional “design and verify” approach to a “specify and synthesize” approach. An overview is given of a subset of the recent advances in the synthesis of reactive control protocols. These techniques are applied in the context of reconfiguration of the networks in reaction to the changes in their operating environment. These automatically synthesized control protocols are also validated on high-fidelity simulationmodels and on an academic-scale hardware testbed.
Cerebrospinal fluid tau/beta-amyloid(42) ratio as a prediction of cognitive decline in nondemented older adults.

To investigate the ability of cerebrospinal fluid (CSF) and plasma measures to discriminate early-stage Alzheimer disease (AD) (defined by clinical criteria and presence/absence of brain amyloid) from nondemented aging and to assess whether these biomarkers can predict future dementia in cognitively normal individuals.



Evaluation of CSF beta-amyloid(40) (Abeta(40)), Abeta(42), tau, phosphorylated tau(181), and plasma Abeta(40) and Abeta(42) and longitudinal clinical follow-up (from 1 to 8 years).



Longitudinal studies of healthy aging and dementia through an AD research center.



Community-dwelling volunteers (n = 139) aged 60 to 91 years and clinically judged as cognitively normal (Clinical Dementia Rating [CDR], 0) or having very mild (CDR, 0.5) or mild (CDR, 1) AD dementia.



Individuals with very mild or mild AD have reduced mean levels of CSF Abeta(42) and increased levels of CSF tau and phosphorylated tau(181). Cerebrospinal fluid Abeta(42) level completely corresponds with the presence or absence of brain amyloid (imaged with Pittsburgh Compound B) in demented and nondemented individuals. The CSF tau/Abeta(42) ratio (adjusted hazard ratio, 5.21; 95% confidence interval, 1.58-17.22) and phosphorylated tau(181)/Abeta(42) ratio (adjusted hazard ratio, 4.39; 95% confidence interval, 1.62-11.86) predict conversion from a CDR of 0 to a CDR greater than 0.



The very mildest symptomatic stage of AD exhibits the same CSF biomarker phenotype as more advanced AD. In addition, levels of CSF Abeta(42), when combined with amyloid imaging, augment clinical methods for identifying in individuals with brain amyloid deposits whether dementia is present or not. Importantly, CSF tau/Abeta(42) ratios show strong promise as antecedent (preclinical) biomarkers that predict future dementia in cognitively normal older adults.
Crack band theory for fracture of concrete

A fracture theory for a heterogeneous aggregate material which exhibits a gradual strainsoftening due to microcracking and contains aggregate pieces that are not necessarily small compared to struttural dimensions is developed. Only Mode I is considered. The fracture is modeled as a blunt smeared crack band, which is justified by the random nature of the microstructure. Simple triaxial stress-strain relations which model the strain-softening and describe the effect of gradual microcracking in the crack band are derived. It is shown that it is easier to use compliance rather than stiffness matrices and that it suffices to adjust a single diagonal term of the compliance matrix. The limiting case of this matrix for complete (continuous) cracking is shown to be identical to the inverse of the well-known stiffness matrix for a perfectly cracked material. The material fracture properties are characterized by only three paPlameters -fracture energy, uniaxial strength limit and width of the crack band (fracture Process zone), while the strain-softening modulus is a function of these parameters. A m~thod of determining the fracture energy from measured complete stressstrain relations is' also given. Triaxial stress effects on fracture can be taken into account. The theory is verljied by comparisons with numerous experimental data from the literature. Satisfactory fits of maximum load data as well as resistance curves are achieved and values of the three matetial parameters involved, namely the fracture energy, the strength, and the width of crack b~nd front, are determined from test data. The optimum value of the latter width is found to be about 3 aggregate sizes, which is also justified as the minimum acceptable for a homogeneous continuum modeling. The method of implementing the theory in a finite element code is al$o indicated, and rules for achieving objectivity of results with regard to the analyst's choice of element size are given. Finally, a simple formula is derived to predict from the tensile strength and aggregate size the fracture energy, as well as the strain-softening modulus. A statistical analysis of the errors reveals a drastic improvement compared to the linear fracture th~ory as well as the strength theory. The applicability of fracture mechanics to concrete is thz4 solidly established.
Parallelizing Sequential Graph Computations

This paper presents GRAPE, a parallel system for graph computations. GRAPE differs from prior systems in its ability to parallelize existing sequential graph algorithms as a whole. Underlying GRAPE are a simple programming model and a principled approach, based on partial evaluation and incremental computation. We show that sequential graph algorithms can be "plugged into" GRAPE with minor changes, and get parallelized. As long as the sequential algorithms are correct, their GRAPE parallelization guarantees to terminate with correct answers under a monotonic condition. Moreover, we show that algorithms in MapReduce, BSP and PRAM can be optimally simulated on GRAPE. In addition to the ease of programming, we experimentally verify that GRAPE achieves comparable performance to the state-of-the-art graph systems, using real-life and synthetic graphs.
Simultaneous Recognition and Relative Pose Estimation of 3D Objects Using 4D Orthonormal Moments

Both three-dimensional (3D) object recognition and pose estimation are open topics in the research community. These tasks are required for a wide range of applications, sometimes separately, sometimes concurrently. Many different algorithms have been presented in the literature to solve these problems separately, and some to solve them jointly. In this paper, an algorithm to solve them simultaneously is introduced. It is based on the definition of a four-dimensional (4D) tensor that gathers and organizes the projections of a 3D object from different points of view. This 4D tensor is then represented by a set of 4D orthonormal moments. Once these moments are arranged in a matrix that can be computed off-line, recognition and pose estimation is reduced to the solution of a linear least squares problem, involving that matrix and the 2D moments of the observed projection of an unknown object. The abilities of this method for 3D object recognition and pose estimation is analytically proved, demonstrating that it does not rely on experimental work to apply a generic technique to these problems. An additional strength of the algorithm is that the required projection is textureless and defined at a very low resolution. This method is computationally simple and shows very good performance in both tasks, allowing its use in applications where real-time constraints have to be fulfilled. Three different kinds of experiments have been conducted in order to perform a thorough validation of the proposed approach: recognition and pose estimation under z axis (yaw) rotations, the same estimation but with the addition of y axis rotations (pitch), and estimation of the pose of objects in real images downloaded from the Internet. In all these cases, results are encouraging, at a similar level to those of state-of-the art algorithms.
Immunomodulatory therapy for sepsis: an update.

Currently the treatment mainstay of sepsis is early and appropriate antibiotic therapy, accompanied by aggressive fluid administration, the use of vasopressors when needed and the prompt initiation of measures to support each failing organ. Activated protein C and hydrocortisone, when used accordingly can affect mortality. As the pathophysiologic events that take place during sepsis are being elucidated, new molecules that target each step of those pathways are being tested. However, a lot of those molecules affect various mediators of the sepsis cascade including inflammatory cytokines, cellular receptors, nuclear transcription factors, coagulation activators and apoptosis regulators. Over the last decade, a multitude of clinical trials and animal studies have investigated strategies that aimed to restore immune homeostasis either by reducing inflammation or by stimulating the innate and adaptive immune responses. Antibiotics, statins and other molecules with multipotent immunomodulatory actions have also been studied in the treatment of sepsis.
Detection and Antimicrobial Resistance of Vibrio Isolates in Aquaculture Environments: Implications for Public Health.

The aim of this study was to evaluate the presence of Vibrio isolates recovered from four different fish pond facilities in Benin City, Nigeria, determine their antibiogram profiles, and evaluate the public health implications of these findings. Fish pond water samples were collected from four sampling sites between March and September 2014. A total of 56 samples were collected and screened for the isolation of Vibrio species using standard culture-based methods. Polymerase chain reaction (PCR) was used to confirm the identities of the Vibrio species using the genus-specific and species-specific primers. Vibrio species were detected at all the study sites at a concentration on the order of 10(3) and 10(6) CFU/100 ml. A total of 550 presumptive Vibrio isolates were subjected to PCR confirmation. Of these isolates, 334 isolates tested positive, giving an overall Vibrio prevalence rate of 60.7%. The speciation of the 334 Vibrio isolates from fish ponds yielded 32.63% Vibrio fluvialis, 20.65% Vibrio parahaemolyticus, 18.26% Vibrio vulnificus, and 28.44% other Vibrio species. In all, 167 confirmed Vibrio isolates were selected from a pool of 334 confirmed Vibrio isolates for antibiogram profiling. The susceptibility profiles of 20 antimicrobial agents on the isolates revealed a high level of resistance for AMP(R), ERY(R), NAL(R), SUL(R), TMP(R), SXT(R), TET(R), OTC(R), and CHL(R). The percentage of multiple drug resistance Vibrio isolates was 67.6%. The multiple antibiotic resistance index mean value of 0.365 for the Vibrio isolates found in this study indicated that the Vibrio isolates were exposed to high-risk sources of contamination when antibiotics were frequently used. The resistant Vibrio strains could be transmitted through the food chain to humans and therefore constitutes a risk to public health.
Customer-adapted coupon targeting using feature selection

The management of coupon promotions is an important issue for marketing managers since it still is the major promotion medium. However, the distribution of coupons does not go without problems. Although manufacturers and retailers are investing heavily in the attempt to convince as many customers as possible, overall coupon redemption rate is low. This study improves the strategy of retailers and manufacturers concerning their target selection since both parties often end up in a battle for customers. Two separate models are built: one model makes predictions concerning redemption behavior of coupons that are distributed by the retailer while another model does the same for coupons handed out by manufacturers. By means of the feature-selection technique ‘Relief-F’ the dimensionality of the models is reduced, since it searches for the variables that are relevant for predicting the outcome. In this way, redundant variables are not used in the model-building process. The model is evaluated on real-life data provided by a retailer in FMCG. The contributions of this study for retailers as well as manufacturers are threefold. First, the possibility to classify customers concerning their coupon usage is shown. In addition, it is demonstrated that retailers and manufacturers can stay clear of each other in their marketing campaigns. Finally, the feature-selection technique ‘Relief-F’ proves to facilitate and optimize the performance of the models.
Random Linear Network Coding: A free cipher?

We consider the level of information security provided by random linear network coding in network scenarios in which all nodes comply with the communication protocols yet are assumed to be potential eavesdroppers (i.e. "nice but curious"). For this setup, which differs from wiretapping scenarios considered previously, we develop a natural algebraic security criterion, and prove several of its key properties. A preliminary analysis of the impact of network topology on the overall network coding security, in particular for complete directed acyclic graphs, is also included.
Characterization of Backfilling Strategies for Parallel Job Scheduling

Although there is wide agreement that backfilling produces significant benefits in scheduling of parallel jobs, there is no clear consensus on which backfilling strategy is preferable e.g. should conservative backfilling be used or the more aggressive EASY backfilling scheme; should a First-Come First-Served(FCFS) queue-priority policy be used, or some other such as Shortest job First(SF) or eXpansion Factor(XF); In this paper, we use trace-based simulation to address these questions and glean new insights into the characteristics of backfilling strategies for job scheduling. We show that by viewing performance in terms of slowdowns and turnaround times of jobs within various categories based on their width (processor request size), length (job duration) and accuracy of the user’s estimate of run time, some consistent trends may be observed.
Intestinal iron absorption.

Intestinal iron absorption is a critical process for maintaining body iron levels within the optimal physiological range. Iron in the diet is found in a wide variety of forms, but the absorption of non-heme iron is best understood. Most of this iron is moved across the enterocyte brush border membrane by the iron transporter divalent metal-ion transporter 1, a process enhanced by the prior reduction of the iron by duodenal cytochrome B and possibly other reductases. Enterocyte iron is exported to the blood via ferroportin 1 on the basolateral membrane. This transporter acts in partnership with the ferroxidase hephaestin that oxidizes exported ferrous iron to facilitate its binding to plasma transferrin. Iron absorption is controlled by a complex network of systemic and local influences. The liver-derived peptide hepcidin binds to ferroportin, leading to its internalization and a reduction in absorption. Hepcidin expression in turn responds to body iron demands and the BMP-SMAD signaling pathway plays a key role in this process. The levels of iron and oxygen in the enterocyte also exert important influences on iron absorption. Disturbances in the regulation of iron absorption are responsible for both iron loading and iron deficiency disorders in humans.
Pulmonary arterial hypertension in France: results from a national registry.

Pulmonary arterial hypertension (PAH) is an orphan disease for which the trend is for management in designated centers with multidisciplinary teams working in a shared-care approach.



To describe clinical and hemodynamic parameters and to provide estimates for the prevalence of patients diagnosed for PAH according to a standardized definition.



The registry was initiated in 17 university hospitals following at least five newly diagnosed patients per year. All consecutive adult (> or = 18 yr) patients seen between October 2002 and October 2003 were to be included.



A total of 674 patients (mean +/- SD age, 50 +/- 15 yr; range, 18-85 yr) were entered in the registry. Idiopathic, familial, anorexigen, connective tissue diseases, congenital heart diseases, portal hypertension, and HIV-associated PAH accounted for 39.2, 3.9, 9.5, 15.3, 11.3, 10.4, and 6.2% of the population, respectively. At diagnosis, 75% of patients were in New York Heart Association functional class III or IV. Six-minute walk test was 329 +/- 109 m. Mean pulmonary artery pressure, cardiac index, and pulmonary vascular resistance index were 55 +/- 15 mm Hg, 2.5 +/- 0.8 L/min/m(2), and 20.5 +/- 10.2 mm Hg/L/min/m(2), respectively. The low estimates of prevalence and incidence of PAH in France were 15.0 cases/million of adult inhabitants and 2.4 cases/million of adult inhabitants/yr. One-year survival was 88% in the incident cohort.



This contemporary registry highlights current practice and shows that PAH is detected late in the course of the disease, with a majority of patients displaying severe functional and hemodynamic compromise.