Miracle-dz/UniFAR-FTUs huggingface dataset:
A Lightweight Guide on Gibbs Sampling and JAGS

In this document we give some insight about how Gibbs Sampling works and how the JAGS modelling framework implements it. The hope is that, once the reader will have understood these concepts, building a model to perform Bayesian Inference with JAGS should be much easier or, at least, the reader should be more aware of what happens behind the scenes. We assume the reader to have basic knowledge about probability, sufficient to understand the difference between a probability and a probability density. This paper is organized as follows: Section 2, presents the basic principles of Bayesian Inference. Section 3, introduces the JAGS software and its basic modelling principles. Section 3.1, introduces the probabilistic graphical models on which Gibbs Sampling and JAGS are based. Section 4 reports basic definitions about Markov Chains. Section 5 explains Gibbs sampling on the basis of the previously introduced concepts. It gives the rationale behind the method and demonstrates its correctness. Furthermore, it shows how to apply Monte Carlo Integration to the output of Gibbs sampling. Section 6 reports about how JAGS is related to Gibbs sampling. Furthermore, it shows an example written with the R programming language that uses JAGS. The example demonstrates the effectiveness of the complete modelling process. Finally, Section 7 draws the conclusions.
Identification of Clinical and Laboratory Parameters Associated with the Development of Acute Chest Syndrome during Vaso-Occlusive Episodes in Children with Sickle Cell Disease: A Preliminary Step before Assessing Specific and Early Treatment Strategies

This prospective observational study sought to ascertain clinical and laboratory parameters associated with the development of acute chest syndrome (ACS) during vaso-occlusive episodes (VOE) in children with sickle cell disease (SCD). It was performed at the pediatric department of the university Intercommunal Créteil hospital. All children with SCD (all sickle genotypes) consecutively admitted from November 2013 to December 2016 for painful VOEs and no evidence of ACS were included. Clinical and laboratory parameters collected at admission and within 48 h after admission were compared for children in whom ACS developed or not. Variables that were statistically significant on univariate analysis or considered to be clinically relevant were included in a multivariable model to ascertain the risk factors associated with the development of ACS during a VOE. The variables retained in the multivariate model were used to construct a predictive score for ACS. For each included child and during the study period, only data from the first VOE and/or the first ACS were analyzed. Among 191 hospitalizations for painful VOEs, for 176 children with SCD, ACS developed in 35 during hospitalization. Mean hospital stay was longer for children with ACS versus VOEs alone (7.6 (±2.3) vs. 3.3 (±1.8) days, p < 0.0001), and all children with ACS versus 28/156 (17.9%) with VOEs alone received red blood cell transfusion (p < 0.0001). The multivariate model retained pain score (≥9/10), pain localization (abdominal or spinal pain or involving more than two limbs), and high reticulocyte (≥260 × 109/L) and neutrophil (>10 × 109/L) counts, at admission, as independently associated with ACS development. The area under the receiver operating characteristic curve for the ACS predictive score was 0.82 (95% CI: 0.74–0.89), and the negative predictive value was 97.7%. The evolution profiles during the first 48 h differed between children with ACS and VOEs alone, with a more rapid decline of pain score and leucocytosis in children with VOEs. Clinical and laboratory measurements at admission may be simple parameters to identify children with increased risk of ACS development during VOEs and to facilitate early diagnosis of this respiratory complication. Also, the persistent elevation of leukocyte count on day 2 may be considered a sign of evolving ACS.
Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution

The aim of macroevolutionary research is to understand pattern and process in phenotypic evolution and lineage diversification at and above the species level. Historically, this kind of research has been tackled separately by palaeontologists, using the fossil record, and by evolutionary biologists, using phylogenetic comparative methods. Although both approaches have strengths, researchers gain most power to understand macroevolution when data from living and fossil species are analysed together in a phylogenetic framework. This merger sets up a series of challenges – for many fossil clades, well‐resolved phylogenies based on morphological data are not available, while placing fossils into phylogenies of extant taxa and determining their branching times is equally challenging. Once methods for building such trees are available, modelling phenotypic and lineage diversification using combined data presents its own set of challenges. The five papers in this Special Feature tackle a disparate range of topics in macroevolutionary research, from time calibration of trees to modelling phenotypic evolution. All are united, however, in implementing novel phylogenetic approaches to understand macroevolutionary pattern and process in or using the fossil record. This Special Feature highlights the benefits that may be reaped by integrating data from living and extinct species and, we hope, will spur further integrative work by empiricists and theoreticians from both sides of the macroevolutionary divide.
A Simple Model of Bertrand Duopoly with Noisy Prices

We examine a market in which consumers are forced to rely on noisy price signals to select between homogeneous products. The noise originates either from firms' price obfuscation or consumers' bounded information processing capabilities. Standard models and empirical experiments of markets with noise or price obfuscation show that it leads to higher prices detrimental to consumers' welfare. This paper identifies conditions under which an opposite result can be expected. In particular, it shows that a moderate level of noise is beneficial to consumers in a market with a cost leader.
CLASSIFICATION OF VARIOUS LAND FEATURES USING RISAT-1 DUAL POLARIMETRIC DATA

Abstract. Land use land cover classification is one of the widely used applications in the field of remote sensing. Accurate land use land cover maps derived from remotely sensed data is a requirement for analyzing many socio-ecological concerns. The present study investigates the capabilities of dual polarimetric C-band SAR data for land use land cover classification. The MRS mode level 1 product of RISAT-1 with dual polarization (HH & HV) covering a part of Varanasi district, Uttar Pradesh, India is analyzed for classifying various land features. In order to increase the amount of information in dual-polarized SAR data, a band HH + HV is introduced to make use of the original two polarizations. Transformed Divergence (TD) procedure for class separability analysis is performed to evaluate the quality of the statistics prior to image classification. For most of the class pairs the TD values are greater than 1.9 which indicates that the classes have good separability. Non-parametric classifier Support Vector Machine (SVM) is used to classify RISAT-1 data with optimized polarization combination into five land use land cover classes like urban land, agricultural land, fallow land, vegetation and water bodies. The overall classification accuracy achieved by SVM is 95.23 % with Kappa coefficient 0.9350.
Catchment urbanisation and increased benthic algal biomass in streams: linking mechanisms to management

SUMMARY 1. Urbanisation is an important cause of eutrophication in waters draining urban areas. We determined whether benthic algal biomass in small streams draining urban areas was explained primarily by small-scale factors (benthic light, substratum type and nutrient concentrations) within a stream, or by catchment-scale variables that incorporate the interacting multiple impacts of urbanisation (i.e. variables that describe urban density and the intensity of drainage or septic tank systems). 2. Benthic algal biomass was assessed as chlorophyll a density (chl a) in 16 streams spanning a rural–urban gradient, with both a wide range of urban density and of piped stormwater infrastructure intensity on the eastern fringe of metropolitan Melbourne, Australia. The gradient of urban density among streams was broadly correlated with catchment imperviousness, drainage connection (proportion of impervious areas connected to streams by stormwater pipes), altitude, longitude and median phosphorus concentration. Catchment area, septic tank density, median nitrogen concentration, benthic light (photosynthetically active radiation) and substratum type were not strongly correlated with the urban gradient. 3. Variation in benthic light and substratum type within streams explained a relatively small amount of variation in log chl a (3–11 and 1–13%, respectively) compared with between-site variation (39–54%). 4. Median chl a was positively correlated with catchment urbanisation, with a large proportion of variance explained jointly (as determined by hierarchical partitioning) by those variables correlated with urban density. Independent of this correlation, the contributions of drainage connection and altitude to the explained variance in chl a were significant. 5. The direct connection of impervious surfaces to streams by stormwater pipes is hypothesised as the main determinant of algal biomass in these streams through its effect on the supply of phosphorus, possibly in interaction with stormwater-related impacts on grazing fauna. Management of benthic algal biomass in streams of urbanised catchments is likely to be most effective through the application of stormwater management approaches that reduce drainage connection.
Estradiol regulates daily rhythms underlying diet-induced obesity in female mice.

The circadian system is a critical regulator of metabolism and obesity in males, but its role in regulating obesity in females is poorly understood. Since there are sex differences in the development of obesity and susceptibility to obesity-related disorders, we sought to determine the role of estrogens in regulating the circadian mechanisms underlying diet-induced obesity. When fed high-fat diet, C57BL/6J male mice gain weight while females are resistant to diet-induced obesity. Here we demonstrate that estradiol regulates circadian rhythms in females to confer resistance to diet-induced obesity. We found that ovariectomized females with undetectable circulating estrogens became obese and had disrupted daily rhythms of eating behavior and locomotor activity when fed high-fat diet. The phase of the liver molecular circadian rhythm was also altered by high-fat diet feeding in ovariectomized mice. Estradiol replacement in ovariectomized females fed high-fat diet rescued these behavioral and tissue rhythms. Additionally, restoring the daily rhythm of eating behavior in ovariectomized females with time-restricted feeding inhibited diet-induced obesity and insulin resistance. Together, these data suggest that the circadian system is a target for treating obesity and its comorbidities in women after menopause, when circulating levels of estrogens are too low to protect their circadian rhythms.
Enhanced Instantaneous Power Theory with Average Algorithm for Indirect Current Controlled Three-Level Inverter-Based Shunt Active Power Filter under Dynamic State Conditions

An enhanced harmonics extraction algorithm based on Instantaneous Power (PQ) Theory is proposed for indirect current controlled (ICC) three-level neutral point diode clamped (NPC) inverter-based shunt active power filter (SAPF). SAPF is famous in current harmonics mitigation for its flexibility in dealing with dynamic state conditions. As for its controller, PQ Theory has served the major role in harmonics extraction algorithm due to its simple implementation features. However, it suffers from serious time delay due to its dependency on sluggish numerical filters. Furthermore, the algorithm is mostly designed to suit the operation of direct current controlled (DCC) SAPF which requires the knowledge of actual SAPF current (injection current). This leads to inaccurate mitigation as the injection current does not possess the exact information on actual source current which suffers from switching ripples problems. Therefore, two major modifications are introduced involving the development of mathematical average algorithm to replace numerical filter for fundamental real power computation and the formation of mathematical current relationship to change DCC to ICC based operation. The proposed algorithm is developed and evaluated in MATLAB/Simulink. From the simulation results, significant improvement in terms of Total Harmonic Distortion (THD) and response time is presented in comparison to conventional algorithm.
Diversity of Nutrient Content in Grains - A Pilot Metabolomics Analysis

Grains are a major food source providing many essential nutrients. The objective of this work was to determine the biochemical (<1,500 Da) composition of selected grains and grain fractions. We hypothesized that the nutrient composition of grains is not only dependent on the grain type, but also influenced by the milling process to generate individual fractions. Whole grain corn, oat, and wheat were milled and separated into bran and flour/meal fractions. The biochemical composition of the whole grains and their subcomponents were determined by untargeted metabolomic profiling on methanol extracts. This global analysis identified 325 biochemicals, belonging to diverse nutrient categories including carbohydrates, antioxidant, vitamins and amino acids. Many of the metabolites were significantly different between the grain types and grain fractions; statistical analysis showed clear differences in the biochemical composition of corn, oat, and wheat grains. Principle component analysis showed that whole wheat flour and whole oat flour were not distinguishable from their respective grains, while corn meal could be distinguished from the corn grain kernel. Many of these nutrients were decreased in the bran fractions upon processing. This preliminary study provides a glimpse into distinct profiles of different grains and their fractions, which can potentially have an impact on nutrition, health and other parameters. Further research is needed to better understand the health benefits of these compounds in individual grains and grain fractions. The use of metabolomics techniques to better understand the profiles of foods not only can help understand their role in improving their health, but also their impact on food product quality, food safety and other parameters.
Self-assembled thienylsilane molecule as interfacial layer for ZnO nanowire/polymer hybrid system

A thienylsilane molecular layer is self-assembled onto vertically aligned ZnO nanowire templates for promoting in situ electrochemical polymerization of P3HT. The silane functionalization on ZnO surface is investigated using x-ray photoelectron spectroscopy and water contact angle measurements. The silane-based surface modified layer acts as a favorable nucleation site for electrochemical polymerization. We find that the oxidation potential for electrochemical polymerization is obviously decreased compared to that without a surface modifier. The UV-visible absorption in the ZnO nanowire/P3HT film with thienylsilane molecular layer is much stronger than that without surface modification.
THREE-DIMENSIONAL SIMULATION OF MASSIVE STAR FORMATION IN THE DISK ACCRETION SCENARIO

The most massive stars can form via standard disk accretion—despite the radiation pressure generated—due to the fact that the massive accretion disk yields a strong anisotropy in the radiation field, releasing most of the radiation pressure perpendicular to the disk accretion flow. Here, we analyze the self-gravity of the forming circumstellar disk as the potential major driver of the angular momentum transport in the massive disks responsible for the high accretion rates needed for the formation of massive stars. For this purpose, we perform self-gravity radiation hydrodynamic simulations of the collapse of massive pre-stellar cores. The formation and evolution of the resulting circumstellar disk is investigated in (1) axially symmetric simulations using an α-shear-viscosity prescription and (2) a three-dimensional simulation in which the angular momentum transport is provided self-consistently by developing gravitational torques in the self-gravitating accretion disk. The simulation series of different strengths of the α viscosity shows that the accretion history of the forming star is mostly independent of the α-viscosity parameter. The accretion history of the three-dimensional run driven by self-gravity is more time dependent than the viscous disk evolution in axial symmetry. The mean accretion rate, i.e., the stellar mass growth rate, is nearly identical to the α-viscosity models. We conclude that the development of gravitational torques in self-gravitating disks around forming massive stars provides a self-consistent mechanism to efficiently transport angular momentum to outer disk radii. The formation of the most massive stars can therefore be understood in the standard accretion disk scenario.
How much extra information is gained using imputed genotype data

Genotype imputation has been discussed widely as a tool to increase the statistical power associated with genome wide association studies (GWAS) and genomic prediction. Previous studies have examined the performance of imputation by evaluating how well a validation set has been predicted. The aim of this study was to examine the amount of extra information added by utilising genotype imputation. The number of new haplotype combinations, between adjacent loci, was estimated for multiple genotype densities from an Australian Sheep dataset. In our example, using genotypes from OAR6, imputation increased the number of haplotypes for 81% of the regions when imputing from 12k to 50k. Large distances between adjacent low density markers resulted in higher numbers of new haplotypes. This also corresponded to a greater proportion of low frequency haplotypes. When imputing from HD to WGS no information was added for 13% of the regions. The number of new haplotypes was directly related to the number of animals in the reference dataset and the distance between adjacent markers. Estimating the number of new haplotypes from imputation provides an understanding about the value of imputation and can be utilised to help design of reference genotype datasets.
Changes in and the Relationship between Language Learning Motivation and Self-Concept in 11-14 Year-Old Students in Hungary: A Longitudinal Study.

Motivation to learn foreign languages is a significant determinant of successful language acquisition. The subject has been widely researched in the past, and since the early 1990s a great deal of empirical research related to the classroom environment has been proposed to expand theory into everyday classroom practice. I present an empirical, longitudinal (3-year) study to explore the relationship between and changes in foreign language learning motivation, learning motivation and self-concept in the 5th, 6th and 8th forms of elementary school. The same tests (Kozeki-Entwistle’s Learning Motivation Questionnaire, the Tenessee SelfConcept Scale, and Clement, Dornyei and Noels’ Foreign Language Learning Motivation questionnaire) were administered three times, so I was able to compare the results and draw conclusions about developmental tendencies. A strong correlation was found between motivational and self-esteem scores, and between learning and foreign language learning motivation subscales. It is necessary to highlight the importance of the Moral, Family and Social Self, which draws our attention to the family values and beliefs students are equipped with, when they enter the school. The significant decrease in motivation and self-esteem in the period under investigation focuses our attention on problems of adolescence, and challanges language teachers to establish a highly motivating classroom practice.
HECTOR RODRIGUEZ Paper: Flowpoints: A Generative Image Creation Method Using Optical Flow

Flowpoints is a research-creation art project about the experimental exploration of algorithmic processes. Its main focus is the LucasKanade (LK) optical flow algorithm, a technique widely used in computer vision for such purposes as motion tracking and the computation of stereo disparity. Instead of regarding the internal structure of the algorithm as an opaque black box, the Flowpoints project proceeds by opening up the black box and analyzing how LK actually works. The aim is to discover unforeseen effects that can only arise through the experimental visualization/sonification of the data structures and operations constitutive of the algorithm. [1] This presentation will describe in detail the internal structure of the algorithm and the ways it can be subverted for artistic purposes. The outcomes will include abstract line renderings as well as sounds. The latter are generated by computing the formant shifts occuring across two different spectral magnitude envelopes and using this information to deform the original sound samples. [2] This creative methodology thus refuses to regard technology as the transparent conduit of some previously fixed intention. To use the terminology of actor-network theory, technologies now function as mediators rather than intermediaries. [3] The assumption at the heart of the Flowpoints project is that the detailed and systematic exploration, modification, and visualization of an algorithm like LK will suggest novel artistic ideas. Image from Flowpoints. Topic: Algorithmic Art Author: Hector Rodriguez City University of Hong Kong, School of Creative Media Hong Kong References: [1] B. D. Lucas and T. Kanade, “An iterative image registration technique with an application to stereo vision,” Proceedings of Imaging Understanding Workshop, 1981, pp. 12130 [2] Tony Ezzat et al., Morphing Spectral Envelopes Using Audio Flow. http://cbcl.mit. edu/publicati ons/ps/audioflow.pdf [3] Bruno Latour, Pandora’s Hope: Essays on the Reality of Science Studies. Cambridge, Mass. : Harvard University Press, 1999. Contact: smhect@cityu.edu. hk