Miracle-dz/UniFAR-FTUs huggingface dataset:
Biomedical Data Analysis with Prior Knowledge : Modeling and Learning

Modern research in biology and medicine is experiencing a data explosion in quantity and particularly in complexity. Efficient and accurate processing of these datasets demands state-of-the-art computational methods such as probabilistic graphical models, graph-based image analysis and many inference/optimization algorithms. However, the underlying complexity of biomedical experiments rules out direct out-of-the-box applications of these methods and requires novel formulation and enhancement to make them amendable to specific problems. This thesis explores novel approaches for incorporating prior knowledge into the data analysis workflow that leads to quantitative and meaningful interpretation of the datasets and also allows for sufficient user involvement. As discussed in Chapter 1, depending on the complexity of the prior knowledge, these approaches can be categorized as constrained modeling and learning. The first part of the thesis focuses on constrained modeling where the prior is normally explicitly represented as additional potential terms in the problem formulation. These terms prevent or discourage the downstream optimization of the formulation from yielding solutions that contradict the prior knowledge. In Chapter 2, we present a robust method for estimating and tracking the deuterium incorporation in the time-resolved hydrogen exchange (HX) mass spectrometry (MS) experiments with priors such as sparsity and sequential ordering. In Chapter 3, we introduce how to extend a classic Markov random field (MRF) model with a shape prior for cell nucleus segmentation. The second part of the thesis explores learning which addresses problems where the prior varies between different datasets or is too difficult to express explicitly. In this case, the prior is first abstracted as a parametric model and then its optimum parametrization is estimated from a training set using machine learning techniques. In Chapter 4, we extend the popular Rand Index in a cost-sensitive fashion and the problem-specific costs can be learned from manual scorings. This set of approaches becomes more interesting when the input/output becomes structured such as matrices or graphs. In Chapter 5, we present structured learning for cell tracking, a novel approach that learns optimum parameters automatically from a training set and allows for the use of a richer set of features which in turn affords improved tracking performance. Finally, conclusions and outlook are provided in Chapter 6.
Caries on Permanent Teeth: A Non‐parametric Bayesian Analysis

Most earlier epidemiological investigations of dental caries have been based on cross‐sectional data. Subject‐specific information of dental caries in the past, and the duration of exposure of each tooth to the oral environment, are obviously important factors also influencing the presence of dental caries in the future. This has led us to consider multivariate survival models in which the information about the tooth eruption and failure times are combined to assess caries risk. A non‐parametric Bayesian intensity model is presented, reflecting, on the one hand, the within subject and between subject sources of variability, and a corresponding split of variability when considering the 28 permanent teeth. We analyse a data set consisting of the dental history of 240 boys, where the observations are based on predetermined dental examinations taking place approximately once every year. Markov chain Monte Carlo integration techniques are applied in the numerical work.
Evolution and Environment of Early-Type Galaxies

Chemical abundance indicators are studied using composite spectra, which we provide in tabular form. Tables of line strengths measured from these spectra and parameters derived from these line strengths are also provided. From these we find that at fixed luminosity, early-type galaxies in low-density environments are slightly bluer, with stronger O II emission and stronger Hδ and Hγ Balmer absorption lines, indicative of star formation in the not very distant past. These galaxies also tend to have systematically weaker D4000 indices. The Lick indices and α-element abundance indicators correlate weakly but significantly with environment. For example, at fixed velocity dispersion, Mg is weaker in early-type galaxies in low-density environments by 30% of the rms scatter across the full sample, whereas most Fe indicators show no significant environmental dependence. The galaxies in our sample span a redshift range that corresponds to look-back times of ∼1 Gyr. We see clear evidence for evolution of line-index strengths over this time. Since the low-redshift population is almost certainly a passively aged version of the more distant population, age is likely the main driver for any observed evolution. We use the observed redshift evolution as a model-independent clock to identify indicators that are more sensitive to age than to other effects such as metallicity. In principle, for a passively evolving population, comparison of the trends with redshift and environment constrain how strongly the luminosity-weighted ages and metallicities depend on environment. We develop a method for doing this that does not depend on the details of stellar population synthesis models. Our analysis suggests that the galaxies that populate the densest regions in our sample are older by ∼1 Gyr than objects of the same luminosity in the least dense regions, and that metallicity differences are negligible. We also use single-burst stellar population synthesis models, which allow for nonsolar α-element abundance ratios, to interpret our data. The combination of Hβ, Mg b, and ⟨Fe⟩ lines suggests that age, metallicity, and α-enhancement all increase with velocity dispersion. The objects at lower redshifts are older but have the same metallicities and α-enhancements as their counterparts of the same σ at higher redshifts, as expected if the low-redshift sample is a passively aged version of the sample at higher redshifts. In addition, objects in dense environments are less than 1 Gyr older and α-enhanced by ∼0.02 relative to their counterparts of the same velocity dispersion in less dense regions, but the metallicities show no dependence on environment. This suggests that in dense regions, the stars in early-type galaxies formed at slightly earlier times and on a slightly shorter timescale than in less dense regions. Using HγF instead of Hβ leads to slightly younger ages but the same qualitative differences between environments. In particular, we find no evidence that objects in low-density regions are more metal-rich.
Shape optimization of an autonomous underwater vehicle with a ducted propeller using computational fluid dynamics analysis

ABSTRACT Autonomous Underwater Vehicles (AUVs) provide a useful means of collecting detailed oceano-graphic information. The hull resistance of an AUV is an important factor in determining the power requirements and range of the vehicle. This paper describes a procedure using Computational Fluid Dynamics (CFD) for determining the hull resistance of an AUV under development, for a given propeller rotation speed and within a given range of AUV velocities. The CFD analysis results reveal the distribution of the hydrodynamic values (velocity, pressure, etc.) around the AUV hull and its ducted propeller. The paper then proceeds to present a methodology for optimizing the AUV profile in order to reduce the total resistance. This paper demonstrates that shape optimization of conceptual designs is possible using the commercial CFD package contained in Ansys™. The optimum design to minimize the drag force of the AUV was identified for a given object function and a set of constrained design parameters
Stakeholder competency assessments as predictors of career success

Purpose – The purpose of this paper is to extend the work on 360‐degree assessments as a stakeholder perspective and to support the argument that different competency assessments by different rater groups provide valid predictors of the objective and subjective career success of young professionals.Design/methodology/approach – A 360‐degree assessment tool, the leadership inventory (LI), was completed by 330 individuals as part of their professional development. Eight competencies germane to the performance of young professionals were assessed by self, supervisors, peers, and direct reports. These rater assessments were used to predict one's satisfaction with his/her career, promotions, and salary changes.Findings – Different rater groups assess the competencies differently, and these differences are relevant to career success. The results of object measures of career success held when gender, years of work experience, and two individual difference measures (i.e. proactivity and negative emotions) were co.
A SAMPLE OF SEYFERT-2 GALAXIES WITH ULTRALUMINOUS GALAXY-WIDE NARROW-LINE REGIONS: QUASAR LIGHT ECHOES?

We report the discovery of Seyfert-2 galaxies in SDSS-DR8 with galaxy-wide, ultraluminous narrow-line regions (NLRs) at redshifts z = 0.2–0.6. With a space density of 4.4 Gpc−3 at z ∼ 0.3, these “green beans” (GBs) are amongst the rarest objects in the universe. We are witnessing an exceptional and/or short-lived phenomenon in the life cycle of active galactic nuclei (AGNs). The main focus of this paper is on a detailed analysis of the GB prototype galaxy J2240−0927 (z = 0.326). Its NLR extends over 26 × 44 kpc and is surrounded by an extended NLR. With a total [O iii] λ5008 luminosity of (5.7 ± 0.9) × 1043 erg s−1, this is one of the most luminous NLRs known around any type-2 galaxy. Using VLT/XSHOOTER, we show that the NLR is powered by an AGN, and we derive resolved extinction, density, and ionization maps. Gas kinematics is disturbed on a global scale, and high-velocity outflows are absent or faint. This NLR is unlike any other NLR or extended emission line region known. Spectroscopy with Gemini/GMOS reveals extended, high-luminosity [O iii] emission also in other GBs. WISE 24 μm luminosities are 5–50 times lower than predicted by the [O iii] fluxes, suggesting that the NLRs reflect earlier, very active quasar states that have strongly subsided in less than a galaxy's light-crossing time. These light echoes, or ionization echoes, are about 100 times more luminous than any other such echo known to date. X-ray data are needed for photoionization modeling and to verify the light echoes.
Foot Involvement - A Presenting Feature for Gaucher Disease, A Case Report

Introduction: Gaucher disease is one of recessive autosomal diseases, wide range of childhood diseases to the absence of symptoms throughout its life. That three types of is more common than other types, that comprises a wide range of clinical findings in childhood and may be seen in different parts of the body but Long bone involvement is common in Gaucher disease. Case Presentation: In this paper, 11-month-old baby girl suddenly lost the ability to walk and her loss of appetite, night sweats, severe irritability and weight reduction, Her parents were healthy and there was not a history of any special disease in both families and She hasn’t had a history of previous hospitalization, so using different tests and biopsies the Gaucher disease was diagnosed. Conclusions: Careful consideration of signs and symptoms and medical history, with a thorough review of systems, is important when evaluating patients with lysosomal storage disorders. Signs such as splenomegaly, anemia, thrombocytopenia and developmental delay can be signs of Gaucher disease, so the presence of these signs should be investigated.
Stellar parametrization from Gaia RVS spectra

Among the myriad of data collected by the ESA Gaia satellite, about 150 million spectra will be delivered by the Radial Velocity Spectrometer (RVS) for stars as faint as G_RVS~16. A specific stellar parametrization will be performed for most of these RVS spectra. Some individual chemical abundances will also be estimated for the brightest targets. We describe the different parametrization codes that have been specifically developed or adapted for RVS spectra within the GSP-spec working group of the analysis consortium. The tested codes are based on optimization (FERRE and GAUGUIN), projection (MATISSE) or pattern recognition methods (Artificial Neural Networks). We present and discuss their expected performances in the recovered stellar atmospheric parameters (Teff, log(g), [M/H]) for B- to K- type stars. The performances for the determinations of [alpha/Fe] ratios are also presented for cool stars. For all the considered stellar types, stars brighter than G_RVS~12.5 will be very efficiently parametrized by the GSP-spec pipeline, including solid estimations of [alpha/Fe]. Typical internal errors for FGK metal-rich and metal-intermediate stars are around 40K in Teff , 0.1dex in log(g), 0.04dex in [M/H], and 0.03dex in [alpha/Fe] at G_RVS=10.3. Similar accuracies in Teff and [M/H] are found for A-type stars, while the log(g) derivation is more accurate. For the faintest stars, with G_RVS>13-14, a spectrophotometric Teff input will allow the improvement of the final GSP-spec parametrization. The reported results show that the contribution of the RVS based stellar parameters will be unique in the brighter part of the Gaia survey allowing crucial age estimations, and accurate chemical abundances. This will constitute a unique and precious sample for which many pieces of the Milky Way history puzzle will be available, with unprecedented precision and statistical relevance.
Nonparametric Estimation of the Leverage Effect: A Trade-Off Between Robustness and Efficiency

ABSTRACT We consider two new approaches to nonparametric estimation of the leverage effect. The first approach uses stock prices alone. The second approach uses the data on stock prices as well as a certain volatility instrument, such as the Chicago Board Options Exchange (CBOE) volatility index (VIX) or the Black–Scholes implied volatility. The theoretical justification for the instrument-based estimator relies on a certain invariance property, which can be exploited when high-frequency data are available. The price-only estimator is more robust since it is valid under weaker assumptions. However, in the presence of a valid volatility instrument, the price-only estimator is inefficient as the instrument-based estimator has a faster rate of convergence.We consider an empirical application, in which we study the relationship between the leverage effect and the debt-to-equity ratio, credit risk, and illiquidity. Supplementary materials for this article are available online.
Simulation of the future sea level contribution of Greenland with a new glacial system model

Abstract. We introduce the coupled model of the Greenland glacial system IGLOO 1.0, including the polythermal ice sheet model SICOPOLIS (version 3.3) with hybrid dynamics, the model of basal hydrology HYDRO and a parameterization of submarine melt for marine-terminated outlet glaciers. The aim of this glacial system model is to gain a better understanding of the processes important for the future contribution of the Greenland ice sheet to sea level rise under future climate change scenarios. The ice sheet is initialized via a relaxation towards observed surface elevation, imposing the palaeo-surface temperature over the last glacial cycle. As a present-day reference, we use the 1961–1990 standard climatology derived from simulations of the regional atmosphere model MAR with ERA reanalysis boundary conditions. For the palaeo-part of the spin-up, we add the temperature anomaly derived from the GRIP ice core to the years 1961–1990 average surface temperature field. For our projections, we apply surface temperature and surface mass balance anomalies derived from RCP 4.5 and RCP 8.5 scenarios created by MAR with boundary conditions from simulations with three CMIP5 models. The hybrid ice sheet model is fully coupled with the model of basal hydrology. With this model and the MAR scenarios, we perform simulations to estimate the contribution of the Greenland ice sheet to future sea level rise until the end of the 21st and 23rd centuries. Further on, the impact of elevation–surface mass balance feedback, introduced via the MAR data, on future sea level rise is inspected. In our projections, we found the Greenland ice sheet to contribute between 1.9 and 13.0 cm to global sea level rise until the year 2100 and between 3.5 and 76.4 cm until the year 2300, including our simulated additional sea level rise due to elevation–surface mass balance feedback. Translated into additional sea level rise, the strength of this feedback in the year 2100 varies from 0.4 to 1.7 cm, and in the year 2300 it ranges from 1.7 to 21.8 cm. Additionally, taking the Helheim and Store glaciers as examples, we investigate the role of ocean warming and surface runoff change for the melting of outlet glaciers. It shows that ocean temperature and subglacial discharge are about equally important for the melting of the examined outlet glaciers.
The scaling relation between richness and mass of galaxy clusters: a Bayesian approach

We use a sample of 53 galaxy clusters at 0.03 < z < 0.1 with available masses derived from the caustic technique and with velocity dispersions computed using 208 galaxies on average per cluster, in order to investigate the scaling between richness, mass and velocity dispersion. A tight scaling between richness and mass is found, with an intrinsic scatter of only 0.19 dex in mass and with a slope one, i.e. clusters that have twice as many galaxies are twice as massive. When richness is measured without any knowledge of the cluster mass or linked parameters (such as r(200)), it can predict mass with an uncertainty of 0.29 +/- 0.01 dex. As a mass proxy, richness competes favourably with both direct measurements of mass given by the caustic method, which has typically 0.14 dex errors (versus 0.29) and X-ray luminosity, which offers a similar 0.30 dex uncertainty. The similar performances of X-ray luminosity and richness in predicting cluster masses has been confirmed using cluster masses derived from velocity dispersion fixed by numerical simulations. These results suggest that cluster masses can be reliably estimated from simple galaxy counts, at least at the redshift and masses explored in this work. This has important applications in the estimation of cosmological parameters from optical cluster surveys, because in current surveys clusters detected in the optical range outnumber, by at least one order of magnitude, those detected in X-ray. Our analysis is robust from an astrophysical perspective because the adopted masses are among the most hypothesis-parsimonious estimates of cluster mass and from a statistical perspective, because our Bayesian analysis accounts for terms usually neglected, such as the Poisson nature of galaxy counts, the intrinsic scatter and uncertain errors. The data and code used for the stochastic computation are provided in the paper.
Effect of Altered Prior Knowledge on Passage Recall.

A8STRACT A study was conducted to determine: (1) the relation ships between prior knowledge and passage recall; (2) the effect of a prereading activity (PReP on available knowledge; and (3) the effect of the PReP activity on :. otal comprehension scores. The subjects were 161 sixth grade students from a middle class suburban Long Island, New York, public school district, classified as high-, average-, or low-achieving readers. Two passages were selected from a sixth arade social studies text, from which three key words were chosen as memory probes for free association. Twenty multiple choice que5tions were prepared for each passage as comprehension criteria. The subjects were divided into four experimental conditions, With different combinations of free association, PReP, motivation, distractor,-tee:, and questioning activities. Findings indicated that the PReP activity significantly raised the prior knowledge level, and may also have had some generalized effect on comvrehensi.on, This was particularly evident for the on-level group where the opportunity to "think through" relevant knowledge has the most effect on comprehension. (HTH
Stratospheric water vapour budget and convection overshooting the tropopause: modelling study from SCOUT-AMMA

Abstract. The aim of this paper is to study the impacts of overshooting convection at a local scale on the water distribution in the tropical UTLS. Overshooting convection is assumed to be one of the processes controlling the entry of water vapour mixing ratio in the stratosphere by injecting ice crystals above the tropopause which later sublimate and hydrate the lower stratosphere. For this purpose, we quantify the individual impact of two cases of overshooting convection in Africa observed during SCOUT-AMMA: the case of 4 August 2006 over Southern Chad which is likely to have influenced the water vapour measurements by micro-SDLA and FLASH-B from Niamey on 5 August, and the case of a mesoscale convective system over Air on 5 August 2006. We make use of high resolution (down to 1 km horizontally) nested grid simulations with the three-dimensional regional atmospheric model BRAMS (Brazilian Regional Atmospheric Modelling System). In both cases, BRAMS succeeds in simulating the main features of the convective activity, as well as overshooting convection, though the exact position and time of the overshoots indicated by MSG brightness temperature difference is not fully reproduced (typically 1° displacement in latitude compared with the overshoots indicated by brightness temperature difference from satellite observations for both cases, and several hours shift for the Air case on 5 August 2006). Total water budgets associated with these two events show a significant injection of ice particles above the tropopause with maximum values of about 3.7 ton s−1 for the Chad case (4 August) and 1.4 ton s−1 for the Air case (5 August), and a total upward cross tropopause transport of about 3300 ton h−1 for the Chad case and 2400 ton h−1 for the Air case in the third domain of simulation. The order of magnitude of these modelled fluxes is lower but comparable with similar studies in other tropical areas based on models. These two estimations exhibit significant differences and highlight variability among the cases of the impact of overshooting convection in hydrating the lower stratosphere. We show that the regional enhancement of water above the tropopause is between 0.21 to 0.67 ppmv between 380 and 400 K, generally in the range of other model estimations. The amount of water which remains in the stratosphere after the overshoot is estimated for both cases. A range of 330 to 507 tons is found for the Chad case and an upper limit of 200 tons is found for the Air case. Finally we emphasize that the hydrated area in the LS by overshooting convection can be advected relatively far away from the overshoot initial location, with locally mixing ratios of more than 3 ppmv higher than the background level, which is compatible with the balloon borne measurements performed above Niamey in the same air mass, 30 h after the overshoot.