Miracle-dz/UniFAR-FTUs huggingface dataset:
A simultaneous maximum likelihood approach for galaxy--galaxy lensing and cluster lens reconstruction

In a previous paper we investigated means for constraining the mass distribution of cluster galaxies by weak lensing. We concluded that a comprehensive method should treat the lensing effects of individual cluster galaxies and those resulting from a general cluster component simultaneously. To this end we now develop a non-parametric maximum likelihood cluster reconstruction algorithm that can implicitly take into account the presence of cluster galaxies. The method includes an entropy-like regularization prescription and directly uses the ellipticities of individual source galaxy images as observables rather than relying on an averaged ellipticity field. The mass distribution of cluster galaxies is described by parametrized models. For each set of galaxy parameters the cluster reconstruction algorithm allows us to determine the best representation of the global underlying cluster component that is consistent with the presence of the cluster galaxies and the observed image ellipticities of background galaxies. Tests with simulations yield convincing and robust results. We apply the method to a WFPC2 image of the cluster Cl0939+4713, and obtain a detection of the lensing effects of luminous elliptical cluster galaxies. We consider this application as a successful test of our technique. However, the small size of the image we analysed does not yet allow us to draw strong conclusions regarding the mass distribution of cluster galaxies.
Rational certificates of positivity on compact semialgebraic sets

Schm\"udgen's Theorem says that if a basic closed semialgebraic set K = {g_1 \geq 0, . , g_s \geq 0} in R^n is compact, then any polynomial f which is strictly positive on K is in the preordering generated by the g_i's. Putinar's Theorem says that under a condition stronger than compactness, any f which is strictly positive on K is in the quadratic module generated by the g_i's. In this note we show that if the g_i's and the f have rational coefficients, then there is a representation of f in the preordering with sums of squares of polynomials over Q. We show that the same is true for Putinar's Theorem as long as we include among the generators a polynomial N - \sum X_i^2, N a natural number.
The verification method of MASOES applied to the social force model for pedestrian dynamics

MASOES is a multiagent architecture for designing and modeling self-organizing and emergent systems. The architecture describes the elements, relationships and mechanisms, both at the individual and the collective levels, which determine the self-organizing and emergent phenomena, without mathematically modeling the system. In this work is tested a method of verification for MASOES, in order to determine its quality to describe the self-organizing and emergent behavior of real systems. This method is based on the wisdom of crowd paradigm and fuzzy cognitive maps. The case study is based on social force model for pedestrian dynamics, in order to study its behavior and determine its self-organizing and emergent capacity through MASOES.
The treatment of phantom limb pain using immersive virtual reality: Three case studies

Purpose. This paper describes the design and implementation of a case study based investigation using immersive virtual reality as a treatment for phantom limb pain. Method. Three participants who experienced phantom limb pain (two with an upper-limb amputation, and one with a lower-limb amputation) took part in between 2 and 5 immersive virtual reality (IVR) sessions over a 3-week period. The movements of participants' anatomical limbs were transposed into the movements of a virtual limb, presented in the phenomenal space of their phantom limb. Results. Preliminary qualitative findings are reported here to assess proof of principle for this IVR equipment. All participants reported the transferal of sensations into the muscles and joints of the phantom limb, and all participants reported a decrease in phantom pain during at least one of the sessions. Conclusion. The authors suggest the need for further research using control trials.
RR Lyrae: Theory versus Observation

The luminosities, effective temperatures, and metallicities that are derived empirically by Kovács & Jurcsik from the light curves of a large number of globular cluster and field RRab and RRc stars are compared to theoretical RR Lyrae models. The strong luminosity dependence of the empirical blue and red edges (log L vs. log Teff diagram) is in disagreement with that of both radiative and convective models. A reexamination of the theoretical uncertainties in the modeling leads us to conclude that the disagreement appears irreconcilable.
Differential Regulation of Killer Cell Lectin-Like Receptor G1 Expression on T Cells 1

The killer cell lectin-like receptor G1 (KLRG1) is the mouse homologue of the rat mast cell function-associated Ag and contains a tyrosine-based inhibitory motif in its cytoplasmic domain. It has been demonstrated that KLRG1 is induced on activated NK cells and that KLRG1 can inhibit NK cell effector functions. In this study, we show that in naive C57BL/6 mice KLRG1 is expressed on a subset of CD44highCD62Llow T cells. KLRG1 expression can be detected on a small number of Vα14i NK T cells but not on CD8αα+ intraepithelial T cells that are either TCRγδ+ or TCRαβ+. We also show that KLRG1 expression is dramatically induced on ∼50% of the CD8+ T cells during both a viral and a parasitic infection. Interestingly, during Toxoplasma gondii infection, KLRG1 is up-regulated on CD4+ T cells. Although KLRG1 expression can be induced on both NK cells and T cells, the molecular mechanism leading to the induction of KLRG1 differs in these two subsets of cells. Indeed, the up-regulation of KLRG1 on NK cells can be driven in vivo by cytokines, whereas KLRG1 cannot be induced on CD8+ T cells by cytokines. In addition, although induction of KLRG1 on T cells appears to require TCR engagement in vivo, TCR engagement is not sufficient for KLRG1 induction in vitro. Taken together, these data suggest that the expression and induction of KLRG1 on T cells are tightly regulated. This could have important biological consequences on T cell activation and homeostasis.
COMPARISON OF THEORIES FOR ACOUSTIC WAVE PROPAGATION IN GASSY MARINE SEDIMENTS

More than three decades ago, Anderson and Hampton (1, 2) (A&H) presented theories for wave propagation in gassy water, saturated sediments and gassy sediments in their two-part review, which has been cited by many researchers in the geoacoustics and underwater acoustics areas. They gave an empirical formulation based on the theory of Spitzer (3) for the wave propagation in gassy water by adapting that for a viscoelastic, lossy medium. Following Leighton (4), this paper presents a theory based on non-stationary nonlinear dynamics of spherical gas bubbles and extends that 2007 paper to include liquid compressibility and thermal damping effects. The paper then shows how that nonlinear formulation can be reduced to the linear limit, and derives the expressions for the damping coefficients, the scattering cross section, the speed of sound and the attenuation, and compares these with the A&H theory. The current formulation has certain advantages over A&H theory such as implementing an energy conservation based nonlinear model for the gas pressure inside the bubble, having no sign ambiguity for the speed of sound formula (which is important when estimating the bubble void fraction) and correcting the ambiguity on the expression for scattering cross section, as identified in the recent work of Ainslie and Leighton (5). Moreover, the theory presented here forms a basis for a nonlinear, time-dependent acoustic estimation model for gas bubble distributions in viscoelastic mediums since it avoids the commonly encountered assumptions on the bubble dynamics such as linearity, steady-state behaviour and monochromaticity.
Erlotinib Inhibits Growth of a Patient-Derived Chordoma Xenograft

Chordomas are rare primary bone tumors that occur along the neuraxis. Primary treatment is surgery, often followed by radiotherapy. Treatment options for patients with recurrence are limited and, notably, there are no FDA approved therapeutic agents. Development of therapeutic options has been limited by the paucity of preclinical model systems. We have established and previously reported the initial characterization of the first patient-derived chordoma xenograft model. In this study, we further characterize this model and demonstrate that it continues to resemble the original patient tumor histologically and immunohistochemically, maintains nuclear expression of brachyury, and is highly concordant with the original patient tumor by whole genome genotyping. Pathway analysis of this xenograft demonstrates activation of epidermal growth factor receptor (EGFR). In vitro studies demonstrate that two small molecule inhibitors of EGFR, erlotinib and gefitinib, inhibit proliferation of the chordoma cell line U-CH 1. We further demonstrate that erlotinib significantly inhibits chordoma growth in vivo. Evaluation of tumors post-treatment reveals that erlotinib reduces phosphorylation of EGFR. This is the first demonstration of antitumor activity in a patient-derived chordoma xenograft model and these findings support further evaluation of EGFR inhibitors in this disease.
A Novel Thinning Algorithm of 3D Image Model Based on Spatial Wavelet Interpolation

In dynamic modeling process of 3D image, too much few characteristics extracted in the binocular stereo vision modeling process cause the cloud characteristics of the model node could not be recovered and low fidelity of the model. In order to solve this problem, this paper presents a thinning algorithm of 3D image model based on improved spatial wavelet interpolation. Firstly, several coordinates of dynamic characteristic nodes are collected by the binocular stereo vision method to compose a characteristic' assemblage which is used to build an interpolation region. Then the characteristic nodes of interpolation are built in the region by the dynamic wavelet recovering method, and modified in direction. Whether the characteristic is reasonable is judged by the modified result. Finally the new characteristic is taken as the vertex to construct a new region and complete the iterative interpolation. Simulation results show that the accuracy error of the interpolation is less than 15 pixels when image interpolation is carried out based on a few characteristics which basically meet the requirements of stability, accuracy and anti-interference ability of 3D interpolation.
WHO Child Growth Standards based on length/height, weight and age

Aim: To describe the methods used to construct the WHO Child Growth Standards based on length/height, weight and age, and to present resulting growth charts. Methods: The WHO Child Growth Standards were derived from an international sample of healthy breastfed infants and young children raised in environments that do not constrain growth. Rigorous methods of data collection and standardized procedures across study sites yielded very high‐quality data. The generation of the standards followed methodical, state‐of‐the‐art statistical methodologies. The Box‐Cox power exponential (BCPE) method, with curve smoothing by cubic splines, was used to construct the curves. The BCPE accommodates various kinds of distributions, from normal to skewed or kurtotic, as necessary. A set of diagnostic tools was used to detect possible biases in estimated percentiles or z‐score curves. Results: There was wide variability in the degrees of freedom required for the cubic splines to achieve the best model. Except for length/height‐for‐age, which followed a normal distribution, all other standards needed to model skewness but not kurtosis. Length‐for‐age and height‐for‐age standards were constructed by fitting a unique model that reflected the 0.7‐cm average difference between these two measurements. The concordance between smoothed percentile curves and empirical percentiles was excellent and free of bias. Percentiles and z‐score curves for boys and girls aged 0–60 mo were generated for weight‐for‐age, length/height‐for‐age, weight‐for‐length/height (45 to 110 cm and 65 to 120 cm, respectively) and body mass index‐for‐age.
Interactive Synthesis Using Free-Form Queries

We present a new code assistance tool for integrated development environments. Our system accepts free-form queries allowing a mixture of English and Java as an input, and produces Java code fragments that take the query into account and respect syntax, types, and scoping rules of Java as well as statistical usage patterns. The returned results need not have the structure of any previously seen code fragment. As part of our system we have constructed a probabilistic context free grammar for Java constructs and library invocations, as well as an algorithm that uses a customized natural language processing tool chain to extract information from free-form text queries. The evaluation results show that our technique can tolerate much of the flexibility present in natural language, and can also be used to repair incorrect Java expressions that contain useful information about the developer's intent. Our demo video is available at http://youtu.be/tx4-XgAZkKU.
MEMS-based handheld single-axis confocal microscope design and experiment

We demonstrate an optical configuration of MEMS based a single-axis confocal microscope imaging setup with 12.7 millimeters diameter commercial lenses. The configuration deploys lens models of optical design software, ZEMAX, to predict optical performance of the actual imaging setup. With this optical design, the maximum field of view is 150 µm × 30 µm with 11.96 µm transverse resolutions and 1.98 mm axial resolution.
VISUAL AUTOMATED MODEL TRANSFORMATION

During the design process of dependable computer controlled systems the verification process aiming to assess whether the system fulfils its requirements or needs some re-design is indispensable at each level of abstraction and after each step of system model refinement in order to spare time and resources. When such a refinement step is performed, system characteristics like dependability, timeliness and correctness are assessed. The characteristics are subsequently confronted with requirements, therefore only provenly correct refinement steps are allowed. Several sophisticated mathematical tools exist supporting the assessment of these system parameters (e.g. SPIN model checker [3], PVS theorem prover [6]). However, special mathematical skills and a thorough knowledge of the underlying mathematics are required for their use. Moreover, additional obstacles (such as problems in the consistency and faithfulness of different sort of models) arise due to the lack of an automated transformation and back-annotation method between the mathematical and designer models. The aim of the ongoing research is to provide a general framework for a visual automated model transformation system providing provenly correct and complete, automatically generated transformation algorithms between UML-based system models and different types of mathematical models [7].
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. This failure limits the application of these methods to RNA and DNA systems. In this work, we provide benchmark ab initio gas-phase two-dimensional potential energy scans of the RNA and DNA sugar puckering. The benchmark calculations are compared with semiempirical models. Pucker corrections are introduced into the semiempirical models via B-spline interpolation of the potential energy difference surface relative to the benchmark data. The corrected semiempirical models are shown to well reproduce the ab initio puckering profiles. Furthermore, we demonstrate that the uncorrected semiempirical models do not usually produce a transition state between the A-form and B-form sugar puckers, but the ab initio transition state is reproduced when the B-spline correction is used.
Aptitude-by-Treatment Interactions in Research on Educational Interventions

A common theme uniting articles in this special issue is a focus on aptitude-by-treatment interactions (ATIs). This timely and welcome focus allows the field to synthesize current substantive findings on ATIs in educational intervention research in both reading and math domains. In this methodological commentary, we begin by reviewing traditional approaches for detecting and reporting interactions in single-level and multilevel models. Next, we discuss some limitations of traditional approaches for theorizing about and modeling ATIs, and we suggest some solutions. These solutions include interpreting level-specific (unconflated) ATIs, understanding and ameliorating threats to adequate power for detecting ATIs, expanding focus beyond linear ATIs, and increasing the number of measurement occasions beyond two to allow use of a growth modeling framework for investigating ATIs. Incorporating some of these advances into future research can motivate new research questions about educational interventions and lead to new discoveries in the search for ATIs.
D-brane networks in flux vacua, generalized cycles and calibrations

We consider chains of generalized submanifolds, as defined by Gualtieri in the context of generalized complex geometry, and define a boundary operator that acts on them. This allows us to define generalized cycles and the corresponding homology theory. Gauge invariance demands that D-brane networks on flux vacua must wrap these generalized cycles, while deformations of generalized cycles inside of a certain homology class describe physical processes such as the dissolution of D-branes in higher-dimensional D-branes and MMS-like instantonic transitions. We introduce calibrations that identify the supersymmetric D-brane networks, which minimize their energy inside of the corresponding homology class of generalized cycles. Such a calibration is explicitly presented for type II = 1 flux compactifications to four dimensions. In particular networks of walls and strings in compactifications on warped Calabi-Yau's are treated, with explicit examples on a toroidal orientifold vacuum and on the Klebanov-Strassler geometry.
MEI: Mutual Enhanced Infinite Community-Topic Model for Analyzing Text-Augmented Social Networks

Community and topic can help summarize the text-augmented social networks. Existing works mixed up community and topic by regarding them as the same. However, there is inherent difference between community and topic such that treating them as the same is not so flexible. We propose a mutual enhanced infinite community-topic model (MEI) to detect communities and topics simultaneously in text-augmented social networks. Community and topic are correlated via community-topic distribution. The mutual enhancement effect between community and topic is validated by introducing two novel measures perplexity with community (perplexityc) and MRK with topic (MRKt). To determine the numbers of communities and topics automatically, Dirichlet Process Mixture model (DPM) and Hierarchical Dirichlet Process mixture model (HDP) are used to model community and topic respectively. We further introduce parameter to model the weight of community and topic responsible for community inference. Experiments on the co-author network built from a subset of DBLP data show MEI outperforms the baseline models in terms of generalization performance. Parameter study shows that MEI is averagely improved by 3.7% and 15.5% in perplexityc and MRKt respectively by setting low weight for topic. We also experimentally validate that MEI can determine the appropriate numbers of communities and topics.
Associations between urinary phthalate concentrations and semen quality parameters in a general population.

STUDY QUESTION Are urinary phthalate concentrations associated with altered semen quality parameters among males recruited from the general population? SUMMARY ANSWER Urinary levels of metabolites of phthalate diesters are associated with lower total sperm counts, larger sperm head sizes, and higher percentages of morphologically abnormal sperm. WHAT IS KNOWN ALREADY High dose experiments in rats implicate phthalates as anti-androgens. Studies involving infertile men seeking care suggest that phthalates influence measures of semen quality raising concern about the implications for men in the general population. STUDY DESIGN, SIZE, DURATION This prospective cohort study comprised 501 male partners in couples discontinuing contraception to become pregnant, who were recruited from 16 US counties using population-based sampling frameworks from 2005 to 2009. PARTICIPANTS/MATERIALS, SETTING, METHODS Urine and semen samples were obtained at baseline from 473 (94%) men, of whom 378 (80%) men provided a second sample the following month. Urine was analyzed for 14 monoester metabolites of phthalate diesters by high-performance liquid chromatography coupled to tandem mass spectrometry. Semen samples were analyzed for 34 quality parameters categorized as general, motility, morphology, sperm head and sperm chromatin structure. MAIN RESULTS AND THE ROLE OF CHANCE Urinary mono-[2-(carboxymethyl) hexyl] phthalate (MCMHP), mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP), mono-benzyl phthalate (MBzP), and mono-isononyl phthalate (MNP) were significantly associated with lower total sperm counts and concentrations, larger sperm head sizes, higher proportions of megalo head sperm morphology, and/or other morphological changes. Urinary mono-methyl phthalate (MMP) and mono-cyclohexyl phthalate (MCPP) were significantly associated with lower sperm motility, and urine mono-2-ethylhexyl phthalate (MEHP) was significantly associated with higher sperm motility. LIMITATIONS, REASONS FOR CAUTION While adverse associations were observed, the implications of the findings for couple fecundity and fertility remain to be established. Cautious interpretation is needed in light of reliance on a single measurement of phthalate measure and no correction for multiple comparisons.
Heterogeneous Network Analysis of Developer Contribution in Bug Repositories

Using a bug repository, developers contribute to improve the quality of software incrementally by creating and updating bug reports. All the software artifacts in bug repositories are derived from developer contribution. Most prior studies on developer contribution in bug repositories bias on one particular form, e.g., commenting bug reports. However, in real practice of bug repositories, developers participate in and contribute to software projects via multiple ways, e.g., reporting new bugs, reopening incorrectly fixed bugs, commenting unfixed bug reports, and fixing unsolved bugs. In this paper, we exploit recent advances in analysis of heterogeneous network to avoid biased aspects in measuring developer contribution and explore multiple types of developer contribution in bug repositories. Further, we consider leveraging such multiple types of developer contribution to assist a typical prediction problem in bug repositories, i.e., bug triage. Empirical studies on bug repositories of Eclipse and Mozilla show that our approach can provide enriched knowledge of developer contribution to improve the resolution of bug triage. This study strongly suggests using the promising aspects of heterogeneous network can open many actionable insights in analyzing software repositories.