nils-herrmann/clean_scirepeval huggingface dataset:
Pixel Level Tissue Classification for Ultrasound Images
Venue: IEEE Journal of Biomedical and Health Informatics

Pixel level tissue classification for ultrasound images, commonly applied to carotid images, is usually based on defining thresholds for the isolated pixel values. Ranges of pixel values are defined for the classification of each tissue. The classification of pixels is then used to determine the carotid plaque composition and, consequently, to determine the risk of diseases (e.g. strokes) and whether or not a surgery is necessary. The use of threshold based methods dates from the early 2000s but it is still widely used for virtual histology.  We propose the use of descriptors that take into account information about a neighborhood of a pixel when classifying it. We evaluated experimentally different descriptors (statistical moments, texture based, gradient based, local binary patterns, etc. on a dataset of five types of tissues: blood, lipids, muscle, fibrous, and calcium. The pipeline of the proposed classification method is based on image normalization, multiscale feature extraction, including the proposal of a new descriptor, and machine learning classification. We have also analyzed the correlation between the proposed pixel classification method in the ultrasound images and the real histology with the aid of medical specialists.  The classification accuracy obtained by the proposed method with the novel descriptor in the ultrasound tissue images (around 73% is significantly above the accuracy of the state of the art threshold based methods (around 54% The results are validated by statistical tests. The correlation between the virtual and real histology confirms the quality of the proposed approach showing it is a robust ally for the virtual histology in ultrasound images.
Do arbuscular mycorrhizal fungi affect cadmium uptake kinetics, subcellular distribution and chemical forms in rice?
Venue: The Science of the total environment

Rice (Oryza sativa L. plants were inoculated with two species of arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices (RI) and Funneliformis mosseae (FM) and grown for 60days to ensure strong colonization. Subsequently, a short term hydroponic experiment was carried out to investigate the effects of AMF on cadmium (Cd) uptake kinetics, subcellular distribution and chemical forms in rice exposed to six Cd levels (0, 0.005, 0.01, 0.025, 0.05, 0.1mM) for three days. The results showed that the uptake kinetics of Cd fitted the Michaelis Menten model well (R(2)>0.89) AMF significantly decreased the Cd concentrations both in shoots and roots in Cd solutions. Furthermore, the decrement of Cd concentrations by FM was significantly higher than RI treatment in roots. AMF reduced the Cd concentrations markedly in the cell wall fractions at high Cd substrate =0.025mM) The main subcellular fraction contributed to Cd detoxification was cell wall at low Cd substrate <0.05mM) while vacuoles at high Cd substrate =0.05mM) Moreover, the concentrations and proportions of Cd in inorganic and water soluble form also reduced by AMF colonization at high Cd substrate =0.05mM) both in shoots and roots. This suggested that AMF could convert Cd into inactive forms which were less toxic. Therefore, AMF could enhance rice resistance to Cd through altering subcellular distribution and chemical forms of Cd in rice.
An Introduction to Survival Analysis Using Stata

An Introduction to Survival Analysis Using Stata, Third Edition provides the foundation to understand various approaches for analyzing time to event data. It is not only a tutorial for learning survival analysis but also a valuable reference for using Stata to analyze survival data. Although the book assumes knowledge of statistical principles, simple probability, and basic Stata, it takes a practical, rather than mathematical, approach to the subject. This updated third edition highlights new features of Stata 11, including competing risks analysis and the treatment of missing values via multiple imputation. Other additions include new diagnostic measures after Cox regression, Statas new treatment of categorical variables and interactions, and a new syntax for obtaining prediction and diagnostics after Cox regression. After reading this book, you will understand the formulas and gain intuition about how various survival analysis estimators work and what information they exploit. You will also acquire deeper, more comprehensive knowledge of the syntax, features, and underpinnings of Statas survival analysis routines.
Rye cover crop effects on maize: A system level analysis

Inclusion of a rye cover crop into maize based systems can offer environmental benefits, but adoption of the practice in the US Midwest is still low. This is related to the possible risk of reduced maize yields following rye. We hypothesized that the magnitude of rye effects on maize yields and drainage water and nitrate (NO3) N losses would be proportionally related to rye biomass. We tested this hypothesis by analyzing data from continuous maize treatments (with and without cover crop) in Iowa, US, that were fertilized following recommendations from late spring nitrate tests. Dataset included measurements (2009 2014) of soil water and temperature, drainage water and NO3 N losses, soil NO3, rye shoot and root biomass and C:N, and maize yields. We supplemented our analysis with a literature review and the use of a cropping systems model (APSIM) to calculate trade offs in system performance characteristics. Experimentally, rye cover crop reduced drainage by 12% and NO3 N losses by 20% (or 31% per unit of N applied) and maize yields by 6% We also found minimal effects on soil temperature, water deficits that reduced yields only during drought years (2012 and 2013) and lower NO3 N losses that were related to reduced NO3 N concentrations in drainage. Results also revealed a linear relationship between drainage and precipitation (r2 0.96) and rye transpiration and shoot biomass (r2 0.84) Model scenario analysis (4 termination dates x 30 years) indicated that rye cover crop decreases NO3 N losses 25.5 26% but does not always reduce drainage water 3.9 13% or grain yields 1.84 6% which is consistent with experimental and literature results. However, analysis of the synthesized measured and simulated dataset do not support a strong relationship between these variables and rye biomass. These results are valuable for decision making and add new fundamental knowledge on rye water and nitrogen use.
Investigation of rye straw ash sintering characteristics and the effect of additives

The understanding of ash sintering during combustion of agricultural residues is far from complete, because of the high heterogeneity of the content and composition of ash forming matters and the complex transformation of them. In order to make agricultural residues competitive fuels on the energy market, further research efforts are needed to investigate agricultural residues' ash sintering behavior and propose relevant anti sintering measures. The aim of this work was to investigate the ash characteristics of rye straw and effects of additives. Three additives were studied regarding their abilities to prevent and abate rye straw ash sintering. Standard ash fusion characterization and laboratory scale sintering tests were performed on ashes from mixtures of rye straw and additives produced at 550degC. Ash residues from sintering tests at higher temperatures were analyzed using a combination of X ray diffraction (XRD) and scanning electron microscopy energy dispersive X ray spectrometry (SEM EDX) High sintering and melting tendency of the rye straw ash at elevated temperatures was observed. Severe sintering of the rye straw ash was attributed to the formation and fusion of low temperature K silicates and K phosphates with high K/Ca ratios. Among the three additives, calcite served the best one to mitigate sintering of the rye straw ash. Ca from the calcite promoted formation of high temperature silicates and calcium rich K phosphates. In addition, calcite may hinder aggregating of ash melts and further formation of large ash slag. Therefore, the chemical reactions and physical restraining effects arose by calcite addition contributed to reduction of ash melts and sintering degree. Upon addition of kaolin, compositions of rye straw ash shifted from low temperature melting K silicates to high temperature melting K Al silicates. The changes of ash chemistry were favorable for reducing sintering of the rye straw ash. As the Ca sludge was added, reduction of sintering of the rye straw ash was less pronounced. Only K4CaSi3O9 and a small amount of KCaPO4 were identified in the rye straw ash as Ca sludge was added.
Multicultural experiences reduce prejudice through personality shifts in Openness to Experience

Across two studies we test the prediction that multicultural experiences reduce intercultural prejudice by increasing Openness to Experience. In Study 1, frequency of self reported multicultural experiences was associated with greater openness and less ethnic prejudice, and openness explained the relationship between multicultural experiences and ethnic prejudice. In Study 2, we experimentally manipulated a multicultural experience. Compared to those in a control condition, participants exposed to the cultural members and elements of foreign cultures reported being higher in Openness to Experience and expressed less prejudice toward these cultural groups. There was also some evidence that multicultural exposure, through openness, caused secondary transfer effects in prejudice reduction. Our findings suggest that exposure to multicultural environments can improve intercultural attitudes by personality shifts in Openness to Experience.
Getting aesthetic chills from music: The connection between openness to experience and frisson

Earlier research has emphasized the emotional nature of frisson (pleasurable aesthetic chills) and has suggested that the personality trait Openness to Experience may predict more frisson episodes. The present study tested these notions by administering a measure of Openness and inducing actual instances of frisson using musical stimuli. One hundred college students completed the NEO PI R, which assesses the five factors of personality (Openness, Extraversion, Neuroticism, Agreeableness, and Conscientiousness) and then listened to five musical selections that were likely to elicit frisson. Frisson was assessed via a combined self report and physiological (galvanic skin response) measure. As predicted, frequency of frisson was positively correlated with overall Openness to Experience, as well as five of its six subfacets: Fantasy, Aesthetics, Feelings, Ideas, and Values. Examination of the more specific relationships suggests the possibility that cognitive attentiveness to music may be more closely related to frisson than had been emphasized in past research.
Openness to Experience Rather Than Overexcitabilities

Openness to experience is a personality factor in the five factor model of personality, and it is composed of six facets. Facets of openness appear conceptually analogous to overexcitabilities (OEs) which are displays of inner energy guiding individuals toward advanced potential according to the theory of positive disintegration. This study examined the similarity of OEs to corresponding openness to experience facets in a sample of 149 creative adolescents and adults and 312 adults from the general population (total N 461) Exploratory structural equation modeling tested competing models in which each OE and corresponding openness facet were modeled as separate factors and as joint factors. The separate factor model had acceptable fit but uninterpretable loadings, while the joint factor model had acceptable fit and interpretable loadings; thus, openness seems to encompass OEs. Accordingly, the field should align with well researched psychological theories like the five factor model of personality and begin to talk about openness rather than OEs.
Openness to Experience and Intellect Differentially Predict Creative Achievement in the Arts and Sciences.
Venue: Journal of personality

The Big Five personality dimension Openness/Intellect is the trait most closely associated with creativity and creative achievement. Little is known, however, regarding the discriminant validity of its two aspects Openness to Experience (reflecting cognitive engagement with perception, fantasy, aesthetics, and emotions) and Intellect (reflecting cognitive engagement with abstract and semantic information, primarily through reasoning) in relation to creativity. In four demographically diverse samples totaling 1,035 participants, we investigated the independent predictive validity of Openness and Intellect by assessing the relations among cognitive ability, divergent thinking, personality, and creative achievement across the arts and sciences. We confirmed the hypothesis that whereas Openness predicts creative achievement in the arts, Intellect predicts creative achievement in the sciences. Inclusion of performance measures of general cognitive ability and divergent thinking indicated that the relation of Intellect to scientific creativity may be due at least in part to these abilities. Lastly, we found that Extraversion additionally predicted creative achievement in the arts, independently of Openness. Results are discussed in the context of dual process theory.
Boundedness, blowup and critical mass phenomenon in competing chemotaxis

We consider the following attraction repulsion Keller Segel system: u t D u kh u v x u w x O t 0 v t D v a u b v x O t 0 0 D w g u d w x O t 0 u x 0 u 0 x v x 0 v 0 x x O with homogeneous Neumann boundary conditions in a bounded domain O R 2 with smooth boundary. The system models the chemotactic interactions between one species (denoted by u and two competing chemicals (denoted by v and w which has important applications in Alzheimer's disease. Here all parameters kh x a b g and d are positive. By constructing a Lyapunov functional, we establish the global existence of uniformly in time bounded classical solutions with large initial data if the repulsion dominates or cancels attraction (i.e. x g a kh If the attraction dominates (i.e. x g a kh a critical mass phenomenon is found. Specifically speaking, we find a critical mass m 4 p a kh x g such that the solution exists globally with uniform in time bound if M m and blows up if M m and M 4 p m th m N where N denotes the set of positive integers and M O u 0 d x the initial cell mass.
Critical Mass How One Thing Leads To Another

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Critical mass for infinite time aggregation in a chemotaxis model with indirect signal production

We study the Neumann initial boundary problem for the chemotaxis system \left\\begin{array}{ll} u_t= \Delta u \nabla \cdot (u\nabla v) x\in \Omega, t>0, 0=\Delta v \mu(t)+w, x\in \Omega, t>0, \tau w_t \delta w u, x\in \Omega, t>0, \end{array} \right. \qquad \qquad \star) in the unit disk \Omega:=B_1(0)\subset \R^2$ where \delta\ge 0$ and \tau>0$ are given parameters and \mu(t)\mint_\Omega w(x,t)dx$ $t>0$ It is shown that this problem exhibits a novel type of critical mass phenomenon with regard to the formation of singularities, which drastically differs from the well known threshold property of the classical Keller Segel system, as obtained upon formally taking \tau\to 0$ in that it refers to blow up in infinite time rather than in finite time: Specifically, it is first proved that for any sufficiently regular nonnegative initial data $u_0$ and $w_0$ \star$ possesses a unique global classical solution. In particular, this shows that in sharp contrast to classical Keller Segel type systems reflecting immediate signal secretion by the cells themselves, the indirect mechanism of signal production in \star$ entirely rules out any occurrence of blow up in finite time. However, within the framework of radially symmetric solutions it is next proved that whenever \delta>0$ and \io u_0 8\pi\delta$ one can find initial data such that \io u_0=m$ and such that for the corresponding solution we have \bas |u(\cdot,t)|_{L^\infty(\Omega) \to \infty \qquad \mbox{as} t\to\infty.
The critical mass ratio of double white dwarf binaries for violent merger induced Type Ia supernova explosions

Mergers of carbon oxygen (CO) white dwarfs (WDs) are considered as one of the potential progenitors of type Ia supernovae (SNe Ia) Recent hydrodynamical simulations showed that the less massive (secondary) WD violently accretes onto the more massive (primary) one, carbon detonation occurs, the detonation wave propagates through the primary, and the primary finally explodes as a sub Chandrasekhar mass SN Ia. Such an explosion mechanism is called the violent merger scenario. Based on the smoothed particle hydrodynamics (SPH) simulations of merging CO WDs, we derived more stringent critical mass ratio (qcr) leading to the violent merger scenario than the previous results. We conclude that this difference mainly comes from the differences in the initial condition, synchronously spinning of WDs or not. Using our new results, we estimated the brightness distribution of SNe Ia in the violent merger scenario and compared it with previous studies. We found that our new qcr does not significantly affect the brightness distribution. We present the direct outcome immediately following CO WD mergers for various primary masses and mass ratios. We also discussed the final fate of the central system of the bipolar planetary nebula Henize 2 428, which was recently suggested to be a double CO WD system whose total mass exceeds the Chandrasekhar limiting mass, merging within the Hubble time. Even considering the uncertainties in the proposed binary parameters, we concluded that the final fate of this system is almost certainly a sub Chandrasekhar mass SN Ia in the violent merger scenario.
A threshold covering flow based location model to build a critical mass of alternative fuel stations

To facilitate the transition to alternative fuel vehicles (AFVs) researchers have developed models for optimally locating an initial refueling infrastructure for AFVs with limited driving range. Recently, clustering of stations has emerged as a strategy to encourage consumers to purchase AFVs by building a critical mass of stations. Clustering approaches, however, have focused on serving demands represented as nodes or arcs rather than origin destination (O D) trips. This study proposes a Threshold Coverage extension to the original Flow Refueling Location Model that focuses on the percentage of a zone's O D trips that can be successfully completed given a typical driving range and location of stations. It is motivated by the idea that drivers in an area will not purchase an AFV unless a critical mass of the trips they regularly make can be completed. Therefore, the new model optimally locates p refueling stations on a network to maximize the sum of weighted demand of covered origin zones, where "covered" means that the zone exceeds a specified threshold percentage of their total outbound round trips that are refuelable. The model is tested on networks for Orlando and the state of Florida. As the threshold percentage is raised, fewer zones can surpass the threshold. Covered nodes increasingly cluster together, as do stations for serving their O D flows. The model's policy implementation will provide managerial insights for some key concerns of the industry, such as geographic equity vs. critical mass, from a new perspective.
A LIDA cognitive model tutorial
Venue: BICA 2016

Over a decade in the making and described in some seventy five published papers, the LIDA cognitive model is comprehensive, complex, and hard to "wrap one's head around" Here we offer, in tutorial fashion, a current, relatively complete and somewhat detailed, description of the conceptual LIDA model, with pointers to more complete accounts of individual processes in the literature. These descriptions also include some features of the workings of the LIDA model that have not been published previously. The tutorial begins with several short sections designed to ease the reader into the LIDA model. These are followed by an account of the conceptual commitments of the LIDA model. We also include a brief introduction to the LIDA computational model via the LIDA Framework, with pointers to its own tutorial. This is followed by sketches of several of the LIDA based agents developed with the help of the Framework. The tutorial ends with a section on current research activity, which includes a table showing which aspects of the LIDA conceptual model have currently been implemented computationally.
Birefringence microscopy platform for assessing airway smooth muscle structure and function in vivo
Venue: Science Translational Medicine

A birefringence microscopy technique provides structural and functional information about airway smooth muscle in healthy and mild asthmatic subjects. Advanced analysis of asthma Not all individuals who have respiratory reactions to allergens progress to asthma. In this issue, Cho et al. found that although allergic asthmatics and allergic nonasthmatics both experienced inflammation after allergen challenge, asthmatics had more mucin and type 2 cytokines, and allergen specific T cells sampled from the airspace had increased innate type 2 receptors. Using orientation resolved optical coherence tomography, described by Adams et al. they demonstrated that allergic asthmatics also had increased airway smooth muscle mass. This technique allows for in vivo imaging of airway smooth muscle structure and function, which could shed light on the pathogenesis of many respiratory diseases. The inability to visualize airway smooth muscle (ASM) cells in vivo is a major obstacle in understanding their role in normal physiology and diseases. At present, there is no imaging modality available to assess ASM in vivo. Confocal endomicroscopy lacks the penetration depth and field of view, and conventional optical coherence tomography (OCT) does not have sufficient contrast to differentiate ASM from surrounding tissues. We have developed a birefringence microscopy platform that leverages the micro organization of tissue to add further dimension to traditional OCT. We have used this technology to validate ASM measurements in ex vivo swine and canine studies, visualize and characterize volumetric representations of ASM in vivo, and quantify and predict ASM contractile force as a function of optical retardation. We provide in vivo images and volumetric assessments of ASM in living humans and document structural disease variations in subjects with mild asthma. The opportunity to link inflammatory responses to ASM responses and to link ASM responses to clinical responses and outcomes could lead to an increased understanding of diseases of the airway and, ultimately, to improved patient outcomes.