nils-herrmann/clean_scirepeval huggingface dataset:
Computing likelihoods for coalescents with multiple collisions in the infinitely many sites model

One of the central problems in mathematical genetics is the inference of evolutionary parameters of a population (such as the mutation rate) based on the observed genetic types in a finite DNA sample. If the population model under consideration is in the domain of attraction of the classical Fleming–Viot process, such as the Wright–Fisher- or the Moran model, then the standard means to describe its genealogy is Kingman’s coalescent. For this coalescent process, powerful inference methods are well-established. An important feature of the above class of models is, roughly speaking, that the number of offspring of each individual is small when compared to the total population size, and hence all ancestral collisions are binary only. Recently, more general population models have been studied, in particular in the domain of attraction of so-called generalised Λ-Fleming–Viot processes, as well as their (dual) genealogies, given by the so-called Λ-coalescents, which allow multiple collisions. Moreover, Eldon and Wakeley (Genetics 172:2621–2633, 2006) provide evidence that such more general coalescents might actually be more adequate to describe real populations with extreme reproductive behaviour, in particular many marine species. In this paper, we extend methods of Ethier and Griffiths ( 1987) and Griffiths and Tavaré ( 1994a,  1995) to obtain a likelihood based inference method for general Λ-coalescents. In particular, we obtain a method to compute (approximate) likelihood surfaces for the observed type probabilities of a given sample. We argue that within the (vast) family of Λ-coalescents, the parametrisable sub-family of Beta(2 − α, α)-coalescents, where α ∈ (1, 2], are of particular relevance. We illustrate our method using simulated datasets, thus obtaining maximum-likelihood estimators of mutation and demographic parameters.

Field of study: Biology, Mathematics
Expression, crystallization and preliminary X-ray analysis of human and rabbit 20alpha-hydroxysteroid dehydrogenases in complex with NADP(H) and various steroid substrates.

Progesterone plays an essential role in the maintenance of the pregnancy of most mammals. 20alpha-Hydroxysteroid dehydrogenase (20alpha-HSD) catalyses the inactivation of progesterone into its inactive form, 20alpha-hydroxyprogesterone, and could thus be involved in progesterone withdrawal and in the control of gestation. In this report, the purification and crystallization of recombinant human and rabbit 20alpha-HSDs (h20alpha-HSD and rb20alpha-HSD) are described, two highly homologous enzymes possessing, in addition to their common 20alpha-HSD activity, different activities and substrate specificities. Complete diffraction data sets have been collected for crystals of rb20alpha-HSD in complex with NADP(H) and with either dihydrotestosterone (1.8 A), progesterone (1.7 A) or 4-androstenedione (1.8 A). All these crystals belong to the monoclinic space group P2(1). A partial data set has also been collected for a crystal of h20alpha-HSD (P2(1)2(1)2(1)) in complex with NADP(H) and progesterone.

Field of study: Chemistry
The electrical properties of 0.45Li2O·0.55B2O3 glasses doped with Al2O3 or LISICON

The electrical properties of 0.45Li 2 O·0.55B 2 O 3 glasses doped with Al 2 O 3 or LISICON are reported. Al 2 O 3 proved to be partially dissolved in this glass and caused higher activation energy and lower value of electrical conductivity as compared to those of undoped glass. In the case of LISICON dopant the dissolution was complete and changes in electrical properties of LISICON-doped glass were observed.

Field of study: Materials science
The Problems and Counterplans That Exist in University on the Processing of Assessing the Title of Technical Ministration at Present

Evaluation is one of the testing modes about teacher's scholarship level,ability and outstanding achievement.It is also the affirmation of teacher's complex labor.It relates to the benefits of each teacher in school.Now,there are many problems in university on how to select excellent teacher.This paper analyses the problems and brings up the problem-solving counterplans and suggestions.

Field of study: Agricultural and Food sciences
T-Man: Gossip-based fast overlay topology construction

Large-scale overlay networks have become crucial ingredients of fully-decentralized applications and peer-to-peer systems. Depending on the task at hand, overlay networks are organized into different topologies, such as rings, trees, semantic and geographic proximity networks. We argue that the central role overlay networks play in decentralized application development requires a more systematic study and effort towards understanding the possibilities and limits of overlay network construction in its generality. Our contribution in this paper is a gossip protocol called T-Man that can build a wide range of overlay networks from scratch, relying only on minimal assumptions. The protocol is fast, robust, and very simple. It is also highly configurable as the desired topology itself is a parameter in the form of a ranking method that orders nodes according to preference for a base node to select them as neighbors. The paper presents extensive empirical analysis of the protocol along with theoretical analysis of certain aspects of its behavior. We also describe a practical application of T-Man for building Chord distributed hash table overlays efficiently from scratch.

Field of study: Computer science
Approximate Kernel PCA Using Random Features: Computational vs. Statistical Trade-off

Kernel methods are powerful learning methodologies that provide a simple way to construct nonlinear algorithms from linear ones. Despite their popularity, they suffer from poor scalability in big data scenarios. Various approximation methods, including random feature approximation have been proposed to alleviate the problem. However, the statistical consistency of most of these approximate kernel methods is not well understood except for kernel ridge regression wherein it has been shown that the random feature approximation is not only computationally efficient but also statistically consistent with a minimax optimal rate of convergence. In this paper, we investigate the efficacy of random feature approximation in the context of kernel principal component analysis (KPCA) by studying the trade-off between computational and statistical behaviors of approximate KPCA. We show that the approximate KPCA is both computationally and statistically efficient compared to KPCA in terms of the error associated with reconstructing a kernel function based on its projection onto the corresponding eigenspaces. Depending on the eigenvalue decay behavior of the covariance operator, we show that only $n^{2/3}$ features (polynomial decay) or $\sqrt{n}$ features (exponential decay) are needed to match the statistical performance of KPCA. We also investigate their statistical behaviors in terms of the convergence of corresponding eigenspaces wherein we show that only $\sqrt{n}$ features are required to match the performance of KPCA and if fewer than $\sqrt{n}$ features are used, then approximate KPCA has a worse statistical behavior than that of KPCA.

Field of study: Computer science
QUANTIFICATION INDEX RESEARCH FOR THE RATIONALITY OF STRUT-AND-TIE MODEL

The design for the stress discontinuous region in concrete members mainly bases on the experience or requirement of construction in China.It inevitably affects the design quality of concrete.Nowadays,the design method for the concrete stress discontinuous region is based on strut-and-tie model theory in overseas.Concrete design codes for strut-and-tie theory have been adopted by many countries.But there are no quantification indices for the rationality of strut-and-tie models.Bases on the principle of minimum complementary potential energy,propose to take the factor of a complementary potential energy deviation as the quantification index of the rationality of strut-and-tie models.In order to verify the feasibility of the quantification index,take a corbel and a deep beam as examples,the reinforcements design according to different strut-and-tie models.And the feasibility is verified by the examples.The analysis result shows that the factor of the complementary potential energy deviation is very sensitivity to the rationality of strut-and-tie models.It can be taken as a quantification index of the rationality of strut-and-tie models.The superposition algorithm of strut-and-tie models is derived.Some signification conclusions are obtained.

Field of study: Engineering
Contribution of quasiparticle-phonon, recoil and coriolis interactions in describing low-lying states of 133Nd isotope


A quasiparticle-phonon coupling based on one quadrupole phonon is developed. The coupling is constructed by using a deformed average field of Nilsson, a monopole pairing interaction and a quadrupole-quadrupole force. Microscopic structure of the quadrupole phonon is given from the Tamm-Dancoff Approximation. The two effects of recoil and Coriolis forces are included with the assumption of a symmetric rotational motion. Since theoretical treatment is performed for an odd- A nuclei the configuration of intrinsic states should contain both one-quasiparticle and quasiparticle-phonon components. This method is applied to describe the level scheme of 133Nd for which an agreement with experimental data is obtained. The results are also found similar to previous calculations obtained by the Particle plus Triaxial Rotor Model.

Field of study: Physics
Application of advanced process control to carbonation columns in manufacture of soda

The carbonation column used in manufacture of soda ash is not only a multiphase reactor but also a multistage crystallizer.The complex processes include chemical absorption,reactive precipitation,multiphase flow,heat and mass transfer,and other physico-chemical processes taking place in the column. Industrial application of a commercial software of model predictive control(MPC)for five groups of twenty-five carbonation columns in a soda plant was introduced in this paper.An MPC system,which was composed of nearly one hundred controlled variables,manipulated variables and disturbance variables,was developed to deal with the constrained multivariable control problem on-line of the carbonation columns.Industrial application results showed that the MPC software could ensure the best operation for a long time and realize the ultimate highest operation potential of the carbonation systems by reducing the consumption of materials,improving product quality,and minimizing operating cost.

Field of study: Chemistry, Environmental science
Abundant type 10 17 beta-hydroxysteroid dehydrogenase in the hippocampus of mouse Alzheimer's disease model.

A full-length cDNA of mouse type 10 17 beta-hydroxysteroid dehydrogenase (17 beta-HSD10) was cloned from brain, representing the accurate nucleotide sequence information that rendered possible an accurate deduction of the amino acid sequence of the wild-type enzyme. A comparison of sequences and three-dimensional models of this enzyme revealed that structures previously reported by other groups carry either a truncated or mutated amino-terminal sequence. Fusion of the first 11 residues of the wild-type enzyme to the green fluorescent protein directed the reporter protein into mitochondria. Thus, the N-terminus was identified as a mitochondrial targeting signal that accounts for the intracellular localization of the mouse enzyme. This enzyme is normally associated with mitochondria, not with the endoplasmic reticulum as suggested by its trivial name 'endoplasmic reticulum-associated amyloid-beta biding protein (ERAB)'. After its C-terminal region was used to raise rabbit anti-17 betaHSD10 antibodies, immunogold electron microscopy showed that an abundance of this enzyme could be found in hippocampal synaptic mitochondria of betaAPP transgenic mice, but not in normal controls. High levels of this enzyme may disrupt steroid hormone homeostasis in synapses and contribute to synapse loss in the hippocampus of the mouse Alzheimer's disease model.

Field of study: Biology
A Wearable Wireless Electrochemical Instrument Used for In-vivo Neurotransmitter Detection

A wireless electrochemical recording device was developed for the neurotransmitters real-time detection with a low-power microcontroller MSP430 as main control unit, including current detection module, waveform generator module and data transceiver module. This device has a small size (2.3 cm × 1.8 cm × 0.6 cm) and low power consumption. In the experiment, firmware program was designed based on uC/OS operating system and online display and analysis of recording data were carried out by the proposed system combined with the PC software. The system implemented two electroanalytical methods, fast-scan cyclic voltammetry (FSCV) and fixed-potential amperometry, to measure neurotransmitter concentrations at microelectrode. By using fast-scan cyclic voltammetry method, a linear relationship ( R = 0.99) between the concentration of dopamine and response current was acquired in the concentration range of 0.5 × 10 −6 −7.0 × 10 −5 M. In the in-vivo experiments, the electrically evoked dopamine was recorded in the caudate-putamen area of brain in rats. The experimental results show that the system has high detection accuracy, realizing the qualitative and quantitative analysis of brain neurotransmitter.

Field of study: Chemistry
Improving the accuracy of brain tumor surgery via Raman-based technology.

Despite advances in the surgical management of brain tumors, achieving optimal surgical results and identification of tumor remains a challenge. Raman spectroscopy, a laser-based technique that can be used to nondestructively differentiate molecules based on the inelastic scattering of light, is being applied toward improving the accuracy of brain tumor surgery. Here, the authors systematically review the application of Raman spectroscopy for guidance during brain tumor surgery. Raman spectroscopy can differentiate normal brain from necrotic and vital glioma tissue in human specimens based on chemical differences, and has recently been shown to differentiate tumor-infiltrated tissues from noninfiltrated tissues during surgery. Raman spectroscopy also forms the basis for coherent Raman scattering (CRS) microscopy, a technique that amplifies spontaneous Raman signals by 10,000-fold, enabling real-time histological imaging without the need for tissue processing, sectioning, or staining. The authors review the relevant basic and translational studies on CRS microscopy as a means of providing real-time intraoperative guidance. Recent studies have demonstrated how CRS can be used to differentiate tumor-infiltrated tissues from noninfiltrated tissues and that it has excellent agreement with traditional histology. Under simulated operative conditions, CRS has been shown to identify tumor margins that would be undetectable using standard bright-field microscopy. In addition, CRS microscopy has been shown to detect tumor in human surgical specimens with near-perfect agreement to standard H & E microscopy. The authors suggest that as the intraoperative application and instrumentation for Raman spectroscopy and imaging matures, it will become an essential component in the neurosurgical armamentarium for identifying residual tumor and improving the surgical management of brain tumors.

Field of study: Medicine
Extraction of Web Site Evaluation Criteria and Automatic Evaluation

This paper proposes an automated web site evaluation using machine learning to extract evaluation criteria from existing evaluation data. Web site evaluation is a significant task because evaluated web sites provide information useful to users in estimating sites validation and popularity. Although many practical approaches have been taken to present possible measuring sticks for web sites, their evaluation criteria are manually determined. We developed a method to obtain evaluation criteria automatically and rank web sites with the learned classifier. Evaluation criteria are discriminant functions learned from a set of ranking information and evaluation features collected automatically by web robots. Experiments confirmed the effectiveness of our approach and its potential in high-quality web site evaluation.

Field of study: Computer science
Effects of Prior Knowledge, Crowding, and Congruence of Subjects' and Others' Goals on Question Asking in an Unfamiliar Setting

An analysis of how newcomers learn to act in an unfamiliar setting was aimed at uncovering the use of the competence of one particular member of the setting by asking questions of him. The study was designed to test the effects of high vs low setting-specific prior knowledge, high vs low densities and high vs low congruence of subjects' and others' goals in a field setting (career planning and placement center) on both the number of questions asked and social anxiety by 64 first-time users (freshmen). The present study shows that a setting-specific cognitive means, such as prior knowledge, and congruence of subjects' and others' goals reduce the experience of stress from crowding and social anxiety which, in turn, leads to an increase in question-asking. Although there is strong evidence that both prior knowledge and congruence of subjects' and others' goals reduce the newcomer's perception of social anxiety, it is also possible that they enhance the newcomer's knowledge of others' competence which, in turn, affects social anxiety and influences question-asking.

Field of study: Psychology
Towards Self-Organized Anodization of Aluminum in Malic Acid Solutions—New Aspects of Anodization in the Organic Acid

In this work, aluminum (Al) anodization in malic acid electrolytes of different concentrations (0.15 M, 0.25 M, and 0.5 M) was studied. The close-packed hexagonal pore structure was obtained for the first time in this organic acid in a 0.5 M solution, at 250 V and temperature of 5 °C. Moreover, the process was investigated as a function of the number of cycles carried out in the same electrolyte. A repetition of anodization under seemingly the same external electrochemical parameters (applied voltage, temperature, etc.) induced serious changes in the electrolyte. The changes were reflected in the current density vs. time curves and were most evident in the higher concentrated electrolytes. This phenomenon was tentatively explained by a massive incorporation of malate anions into anodic alumina (AAO) framework. The impoverishment of the electrolyte of the malate anions changed internal electrochemical conditions making easier the attraction of the anions to the Al anode and thus the AAO formation. The electrolyte modification was advantageous in terms of pore organization: In a 0.25 M solution, already after the second anodization, the pore arrangement transformed from irregular towards regular, hexagonal close-packed structure. To the best of our knowledge, this is the first observation of this kind.

Field of study: Materials science
Risky business: Changes in boldness behavior in male Siamese fighting fish, Betta splendens, following exposure to an antiandrogen.

Components of boldness, such as activity level and locomotion, influence an individual's ability to avoid predators and acquire resources, generating fitness consequences. The presence of endocrine disrupting chemicals (EDCs) in the aquatic environment may affect fitness by changing morphology or altering behaviors like courtship and exploration. Most research on EDC-generated behavioral effects has focused on estrogen mimics and reproductive endpoints. Far fewer studies have examined the effects of other types of EDCs or measured non-reproductive behaviors. EDCs with antiandrogenic properties are present in waterways yet we know little about their effects on exposed individuals although they may produce effects similar to those caused by estrogen mimics because they act on the same hormonal pathway. To examine the effects of antiandrogens on boldness, this study exposed male Siamese fighting fish, Betta splendens, to a high or low dose of one of two antiandrogens, vinclozolin or flutamide, and observed behavior in three boldness assays, both before and after exposure. Overall, antiandrogen exposure increased boldness behavior, especially following exposure to the higher dose. Whether or not antiandrogen exposure influenced boldness, as well as the nature and intensity of the effect, was assay-dependent. This demonstrates the importance of studying EDC effects in a range of contexts and, at least within this species, suggests that antiandrogenic compounds may generate distinct physiological effects in different situations. How and why the behavioral effects differ from those caused by exposure to an estrogen mimic, as well as the potential consequences of increased activity levels, are discussed. Exposure to an antiandrogen, regardless of dose, produced elevated activity levels and altered shoaling and exploration in male Siamese fighting fish. These modifications may have fitness consequences.

Field of study: Environmental science
Characteristics of tropopause parameters as observed with GPS radio occultation

Characteristics of the lapse rate tropopause are analyzed globally for tropopause altitude and temperature using global positioning system (GPS) radio occultation (RO) data from late 2001 to the end of 2013. RO profiles feature high vertical resolution and excellent quality in the upper troposphere and lower stratosphere, which are key factors for tropopause determination, including multiple ones. RO data provide measurements globally and allow examination of both temporal and spatial tropopause characteristics based entirely on observational measurements. To investigate latitudinal and longitudinal tropopause characteristics, the mean annual cycle, and inter-annual variability, we use tropopauses from individual profiles as well as their statistical measures for zonal bands and 5° × 10° bins. The latitudinal structure of first tropopauses shows the well-known distribution with high (cold) tropical tropopauses and low (warm) extra-tropical tropopauses. In the transition zones (20 to 40° N/S), individual profiles reveal varying tropopause altitudes from less than 7 km to more than 17 km due to variability in the subtropical tropopause break. In this region, we also find multiple tropopauses throughout the year. Longitudinal variability is strongest at northern hemispheric mid latitudes and in the Asian monsoon region. The mean annual cycle features changes in amplitude and phase, depending on latitude. This is caused by different underlying physical processes (such as the Brewer–Dobson circulation – BDC) and atmospheric dynamics (such as the strong polar vortex in the southern hemispheric winter). Inter-annual anomalies of tropopause parameters show signatures of El Nino–Southern Oscillation (ENSO), the quasi–biennial oscillation (QBO), and the varying strength of the polar vortex, including sudden stratospheric warming (SSW) events. These results are in good agreement with previous studies and underpin the high utility of the entire RO record for investigating latitudinal, longitudinal, and temporal tropopause characteristics globally.

Field of study: Environmental science
A note on prevention versus cure.

The aim of this study is to test if the general Swedish population prefers saving lives through prevention or acute care. A trade-off question of a choice between saving lives through prevention or acute care was administered in a Swedish population sample. Based on the answers we estimate the median number of lives saved in acute care that is judged equivalent to saving one life through prevention. According to the results 1.2-1.4 lives saved in acute care is judged equivalent to saving one life through prevention. Thus our results indicate that lives saved through prevention and cure are given about the same value by the median respondent. Individuals seem to focus on the size of the health benefits rather than whether the health benefits are achieved through prevention or cure.

Field of study: Medicine, Political science