Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Analysis of Gene Expression and Genotype Variation Data for Chronic Fatigue Syndrome

In the past few years, high throughput technologies, such as gene expression microarrays and genotyping techniques, have provided efficient ways to measure gene expression levels and genotype variation on a genome-wide scale [Schena et al., 1995; Howell et al., 1999]. Various approaches have been proposed to analyse gene expression data and genotype variation data, in order to discover the complex network of biochemical processes of complex diseases such as chronic fatigue syndrome (CFS) [Presson et al., 2008]. In the analysis of gene expression data, for example, the identification of differentially expressed genes between two groups has been of great interest, and various statistical tests have been conducted [Ghazalpour et al., 2008; Brem et al., 2002; Kang et al., 2008]. In analysing genotype variation data, logistic regression has been commonly used to model the relationship between binary clinical outcomes and discrete predictors, such as genotypes [Henshall & Goddard, 1999; Coffey et al., 2004].
The Pinocchio C++ library : A fast and flexible implementation of rigid body dynamics algorithms and their analytical derivatives

We introduce Pinocchio, an open-source software framework that implements rigid body dynamics algorithms and their analytical derivatives. Pinocchio does not only include standard algorithms employed in robotics (e.g., forward and inverse dynamics) but provides additional features essential for the control, the planning and the simulation of robots. In this paper, we describe these features and detail the programming patterns and design which make Pinocchio efficient. We evaluate the performances against RBDL, another framework with broad dissemination inside the robotics community. We also demonstrate how the source code generation embedded in Pinocchio outperforms other approaches of state of the art.
Left-Symmetric Structures on Simple Modular Lie Algebras

This paper investigates left-symmetric structures on finite-dimensional simple Lie algebras g over a field k. If k is of characteristic 0, then g does not admit any left-symmetric structure. This is known in the theory of affine manifolds. In the modular case, however, such structures may exist. The main purpose of this paper is to show that classical simple Lie algebras of characteristic p > 3 admit left-symmetric structures only in case p divides dim(g). The proof involves the computation of the first cohomology groups of classical Lie algebras for certain g-modules of small dimension. Here g is regarded as the Lie algebra of a connected semisimple algebraic group over an algebraically closed field of characteristic p > 0. Most of these computations are due to Jantzen. For nonrestricted simple Lie algebras of Cartan type it is shown that many more left-symmetric structures can be found. One studies so-called adjoint structures, induced by nonsingular derivations of g. The simple algebra L(G, δ, ƒ) of Block of dimension pn − 1, for example, admits adjoint structures for every p > 0. If p = 2, the results are more complicated.
A Low Noise Preamplifier Circuit for a Highly Sensitive EMAT Transducer for Picometer-scale Ultrasonic Displacement Measurements

We present a novel design of electromagnetic acoustic transducer (EMAT) for non-contact ultrasonic measurements. A recent prototype of the EMAT sensor has miniaturized the receiver size (1.0 cm diameter). It was incorporated with a specially designed low noise preamplifier. Calibration procedures with a Michelson interferometer revealed that the EMAT sensor detected small displacement amplitudes as low as 1.0±0.2 pm in aluminium with a signal bandwidth up to 7.5 MHz (-3dB). Alternatively, this sensitivity figure can be expressed in term of noise-equivalent displacement spectrum as 4.2x10 m.Hz. The absolute sensitivity of the EMAT was 1.98±0.5 V.pm -1 for the detection of longitudinal waves. The paper also presents the comparative study of the performance of the EMAT sensor with various ultrasonic transducers.
Heat Budget in the Kuroshio Extension Region: 1993–99

Abstract Processes responsible for the seasonal and interannual variations of the sea surface temperature as well as of the heat content of the upper ocean (0–400 m) in the Kuroshio Extension region are examined from a 3D advection–diffusion model in finite elements, with an embedded bulk mixed layer. The geostrophic velocity is specified externally from TOPEX/Poseidon altimeter data, and Ekman velocity is specified from NCEP wind stress. The thermal field from the model shows good agreement with observations. While both atmospheric and oceanic processes are required to explain observed nonseasonal SST changes, the interannual heat storage rate is dominated by horizontal advection. In particular, the transition between an elongated and a contracted state of the Kuroshio caused by geostrophic advection has a clear signature in the SST. There is an indication that this process is accompanied by consistent changes in nonseasonal entrainment: when the Kuroshio is in an elongated state and warmer waters are pr.
OBJECT CONTOUR COMPLETION BY COMBINING OBJECT RECOGNITION AND LOCAL EDGE CUES

We developed a top-down and bottom-up segmentation of objects using shape contours through a two-stage procedure.First, the object was identified using an edge-based contour feature and then the object contour was obtained using a constraint optimization procedure based on the results from the earlier identified contours.The initial object detection provides object category specific information for the contour completion to be effected.We argue that top-down bottom-up interaction architecture has plausible neurological correlates.This method has an advantage in that it does not require learning boundaries with large datasets.
Radiomics in glioblastoma: current status, challenges and potential opportunities

Gliomas are tumors which develop in the brain, the most aggressive of which is glioblastoma multiforme (GBM). Despite extensive research to better understand the underlying biology of GBM and advancements in the treatment of this disease, it has an extremely poor prognosis. Poor outcomes in GBM are due to its molecular and clinical heterogeneity, as in other solid tumors. As imaging approaches have been taken to comprehensively characterize tumors, radiomics has emerged as the concept of extracting quantitative radiologic features and drawing associations with clinical outcomes. Radiomics has the potential to improve the predictive ability of radiological datasets. Tumor radiographs are segmented through manual, semi-automated or fully-automated procedures. Segmentation is followed by feature extraction from the tumor volume. Data analysis and predictive modeling are used to relate image-derived features with clinical outcomes. Substantial progress has already been made in solving many of the technical hurdles inherent in the radiomics process. Advances in sequencing, gene expression profiling and machine learning have increased the resolution of datasets and improved the sensitivity and specificity of computational methods used to analyze them. Numerous logistical, computational and clinical challenges remain to unlocking the full potential of the radiomics approach. To make the approach useful in clinical practice, improved statistical models are needed which relate GBM imaging features with patient outcomes with high specificity/sensitivity. More studies correlating radiomic features with disease outcomes and molecular attributes are also needed to illuminate the tumor biology which gives rise to imaging features and underlie response to therapy.
Performing Multi-Temporal Spatial Data Analysis for Coastal Areas and Assessing Thematic Accuracy

It was used TM Landsat images from 1985, 1994, 2004 and 2014 and Object Based Oriented Analysis (OBIA) image classification techniques in order to study changes in land use and land cover for two cities: Passo de Torres and Balneário Gaivota at the south region of Brazil. Based on these analyses, four informational classes were chosen: Natural Vegetation, Water, Urban and Agriculture Use. Agriculture use includes croplands, livestock activities and reforestation areas. It was used post-classification multi-temporal analysis. The aim of this paper is to perform multi-temporal spatial data analysis in order to identify trajectories of changes on land use and land cover, during the last three decades. This paper also discusses an alternative methodology to assess the thematic accuracy in multi-temporal analysis. The multitemporal analysis results show that this study area has considerably changed in the last three decades. The most frequent transition was due to the transformation of natural areas into cropland, livestock and reforestation ones, from the year of 1985 to 2014. It was observed that most of transition for urban class occurred from natural vegetated areas, while few transitions occurred from agricultural areas, even considering these classes as being more representatives in the whole study area. This transition was especially common in coastal urban division into plots of land. Besides understanding those processes of change, this study points out the importance of better planning, licensing and monitoring of urban coast division into plots of land to prevent the continuous loss of natural ecosystems and impoverishment of environmental quality. The accuracy assessment discussion shows the importance in choose a better classification strategy in order to perform the multi-temporal analysis in remote sensed data. Furthermore, it is observed that a considerable amount of research needs to be undertaken before the spatial characterization of thematic accuracy associated with multi-temporal analysis can be adequately reported in standardized format and legends.
Does Preferential Trade Benefit Poor Countries? A General Equilibrium Assessment with Nonhomothetic Preferences

We develop a Ricardian model of trade with nonhomothetic preferences to analyze preferential trade agreements (PTAs) among countries of different stages of economic development. The richer a country is, the more likely will PTAs improve its terms of trade, also when it is a non-member. Rich non-member countries are also less likely to incur welfare losses from PTAs. PTA membership only guarantees welfare gains for countries that are too poor to import the goods rich countries produce. For all other countries, the welfare effects of joining PTAs depend on the world income distribution and on the strength of comparative advantages.
The Edinburgh Feeding Evaluation in Dementia Scale #2 (EdFED #2): convergent and discriminant validity

The increasing feeding difficulty of older people with dementia is well documented (Watson 1993, 1994). However, there is a paucity of validated instruments for the assessment of feeding difficulty in older people with dementia which can be used to guide practice. The scale properties, reliability (Watson 1996) and some aspects of the validity have previously been reported (Watson 1997). This short report describes continuing work on the Edinburgh Feeding Evaluation in Dementia Scale #2 (EdFED #2) and demonstrates the reliability of the EdFED #2 and its convergence with a scale measuring nutritional risk and discrimination from scales measuring unrelated aspects of feeding difficulty.
Chain conditions in computable rings

Friedman, Simpson, and Smith showed that, over RCA 0 , the statements "Every ring has a maximal ideal" and "Every ring has a prime ideal" are equivalent to ACA 0 and WKL 0 , respectively. More recently, Downey, Lempp, and Mileti have shown that, over RCA 0 , the statement "Every ring that is not a field contains a nontrivial ideal" is equivalent to WKLo. In this article we explore the reverse mathematical strength of the classic theorems from commutative algebra which say that every Artinian ring is Noetherian, and every Artinian ring is of finite length. In particular we show that, over RCA 0 , the former implies WKL 0 and is implied by ACA 0 , while over RCA 0 +BΣ 2 , the latter is equivalent to ACA 0 .
Learn From Neighbour: A Curriculum That Train Low Weighted Samples By Imitating

Deep neural networks, which gain great success in a wide spectrum of applications, are often time, compute and storage hungry. Curriculum learning proposed to boost training of network by a syllabus from easy to hard. However, the relationship between data complexity and network training is unclear: why hard example harm the performance at beginning but helps at end. In this paper, we aim to investigate on this problem. Similar to internal covariate shift in network forward pass, the distribution changes in weight of top layers also affects training of preceding layers during the backward pass. We call this phenomenon inverse ”internal covariate shift”. Training hard examples aggravates the distribution shifting and damages the training. To address this problem, we introduce a curriculum loss that consists of two parts: a) an adaptive weight that mitigates large early punishment; b) an additional representation loss for low weighted samples. The intuition of the loss is very simple. We train top layers on ”good” samples to reduce large shifting, and encourage ”bad” samples to learn from ”good” sample. In detail, the adaptive weight assigns small values to hard examples, reducing the influence of noisy gradients. On the other hand, the less-weighted hard sample receives the proposed representation loss. Low-weighted data gets nearly no training signal and can stuck in embedding space for a long time. The proposed representation loss aims to encourage their training. This is done by letting them learn a better representation from its superior neighbours but not participate in learning of top layers. In this way, the fluctuation of top layers is reduced and hard samples also received signals for training. We found in this paper that curriculum learning needs random sampling between tasks for better training. Our curriculum loss is easy to combine with existing stochastic algorithms like SGD. Experimental result shows an consistent improvement over several benchmark datasets.
Cosmological hydrodynamical simulations of galaxy clusters: X-ray scaling relations and their evolution

We analyse cosmological hydrodynamical simulations of galaxy clusters to study the X-ray scaling relations between total masses and observable quantities such as X-ray luminosity, gas mass, X-ray temperature, and Y-X. Three sets of simulations are performed with an improved version of the smoothed particle hydrodynamics GADGET-3 code. These consider the following: non-radiative gas, star formation and stellar feedback, and the addition of feedback by active galactic nuclei (AGN). We select clusters with M-500 > 10(14) M circle dot E(z)(-1), mimicking the typical selection of Sunyaev-Zeldovich samples. This permits to have a mass range large enough to enable robust fitting of the relations even at z similar to 2. The results of the analysis show a general agreement with observations. The values of the slope of the mass-gas mass and mass-temperature relations at z = 2 are 10 per cent lower with respect to z = 0 due to the applied mass selection, in the former case, and to the effect of early merger in the latter. We investigate the impact of the slope variation on the study of the evolution of the normalization. We conclude that cosmological studies through scaling relations should be limited to the redshift range z = 0-1, where we find that the slope, the scatter, and the covariance matrix of the relations are stable. The scaling between mass and Y-X is confirmed to be the most robust relation, being almost independent of the gas physics. At higher redshifts, the scaling relations are sensitive to the inclusion of AGNs which influences low-mass systems. The detailed study of these objects will be crucial to evaluate the AGN effect on the ICM.
Isolation and partial characterization of an acid phosphatase from Artemisia vulgaris pollen extract

An acid phosphatase from an extract of mugwort (Artemisia vulgaris) pollen was pu- rified by a factor of 48 by a combination of ion exchange and gel-chromatography. The molec- ular weights of the enzyme were 76 kDa and 73 kDa, determined by gel filtration on a Sephadex G-100 sf column and by SDS PAGE (under reducing and non-reducing conditions), respectively. In analytical isoelectrofocusing, the enzyme appears as two very close bands, pI at about 4.2. The optimum pH for the enzyme is 5.4. The apparent Km for p-nitrophenyl phos- phate was estimated to be 0.16 mM. The purified enzyme has broad specificity, and hydrolyses p-nitrophenyl phosphate and-naphthyl phosphate. Pyrophosphate and O-phospho-L-tyrosine were estimated to be the best substrates for this enzyme as potential in vivo substrates. The en- zyme is inhibited competitively by phosphate (K i = 1.25 mM), molybdate (K i = 0.055 mM) and pyrophosphate (Ki = 6.7 mM) and non-competitively by fluoride (Ki = 9.8 mM). Metal ions such as Hg 2+ ,C u 2+ and Zn 2+ express an inhibitory effect on the enzyme, while the en- zyme is slightly activated by non-ionic detergents, Tween 20 and Triton X-100. There is no change in the enzyme activity in the presence of tartrate, citrate, EDTA, 1,10-phenanthroline and sulfhydryl-group modifiers such as p-chloromercuribenzoate and N-ethylmaleimide.
Goniospectrophotometric characterization of coatings with diffraction pigments

Coatings with diffraction pigments present high iridescence, which needs to be characterized to describe their appearance. The spectral Bidirectional Reflectance Distribution Function (BRDF) of six coatings with SpectraFlair diffraction pigments were measured using the robot-arm-based goniospectrophotometerer GEFE, designed and developed at CSIC. Principal Components Analysis (PCA) has been applied to study the coatings’ BRDF data. From data evaluation and based in theoretical considerations, we propose a relevant geometric factor to study the spectral reflectance and color gamut variation of coatings with diffraction pigments. At fixed values of this geometrical variable, the spectral BRDF component due to diffraction is almost constant. Commercially-available portable goniospectrophotometers, extensively used in several industries (automotive and others), have to be provided with more aspecular measurement angles to characterize goniochromatic coatings based on diffraction pigments.
Tricholoma giganteum Ameliorates Benzo [ A ] Pyrene – Induced Lung Cancer in Mice

Tricholoma giganteum is a wild edible mushroom, consumed in tropical region of the world and demonstrated to have multiple beneficial effects. We investigated the chemopreventive effect of ethanolic fraction of T. giganteum in mice with acute lung injury induced by Benzo[a]Pyrene. Oral administration of Benzo[a]Pyrene (1 mg/20g body weight) induced marked lung injury, evident from histological and biochemical data. Intraperitoneal administration of ethanolic fraction of T. giganteum (50 mg/kg body weight) significantly overcame the side effect of benzo[a]pyrene by modulation of different antioxidant enzyme and pro/anti-apoptotic gene ratio. Therefore, it could be inferred that alcoholic extract of T. giganteum may hold promise as a chemopreventive agent during the early phases of carcinogenesis.
Rarefied gas flow around a sharp edge induced by a temperature field

Abstract A rarefied gas flow thermally induced around a heated (or cooled) flat plate, contained in a vessel, is considered in two different situations: (i) both sides of the plate are simultaneously and uniformly heated (or cooled); and (ii) only one side of the plate is uniformly heated. The former is known as the thermal edge flow and the latter, typically observed in the Crookes radiometer, may be called the radiometric flow. The steady behaviour of the gas induced in the container is investigated on the basis of the Bhatnagar–Gross–Krook (BGK) model of the Boltzmann equation and the diffuse reflection boundary condition by means of an accurate finite-difference method. The flow features are clarified for a wide range of the Knudsen number, with a particular emphasis placed on the structural similarity between the two flows. The limiting behaviour of the flow as the Knudsen number tends to zero (and thus the system approaches the continuum limit) is investigated for both flows. The detailed structure of the normal stress on the plate as well as the cause of the radiometric force (the force acting on the plate from the hotter to the colder side) is also clarified for the present infinitely thin plate.
LIVING A LIFE ONLINE: TRUST, EXPRESSION, AND INTERACTION IN MMOGS

Life on the Internet has possibly as many forms and functions as real-world existence – a notion that is readily apparent through an examination of virtual worlds and Massively Multiplayer Online Games (MMOGs). In the daily operation of such a world, players face social interactions in much the same fashion that individuals are likely encounter in their offline “real” life (Guadagno, Muscanell, Okdie, Burk, and Ward, 2011). These gaming experiences are of course colored by both the nature of the medium and the unique design of the virtual world in question (Taylor, 1999, 2004; Park and Namho, 2011). Scholars seeking to study the medium itself often look to the ways in which video games affect behavior or facilitate the acquisition of social capital (Zhong, 2011; Collins & Freeman, 2013), while the analysis of specific virtual worlds is traditionally limited to the ethnographic study of social institutions, play communities, and the daily lives of players (Mnookin, 1996; Pearce 2009). This paper is the result of a literature review of social interaction and online communication, as well as a pilot study on MMOG players, examining the relationship between self-disclosure (Miller, Berg, & Archer, 1983), motivation (Yee, 2006), social perception, and resultant behavior. A small pilot study indicated that people’s motivations for gameplay as well as the group memberships of other players affect the likelihood of trusting and helping other players in MMOGs.
Characterization of thermally modified short and long rotation teaks and the effects on coatings performance

Many wood processing industries use short rotation teak, which has lower quality especially in durability and dimensional stability. Heat treatment is an eco-friendly method to improve dimensional stability and durability of wood. The objectives of the study were to investigate the effects of thermal modification on chemical composition, colour, dimensional stability and durability as well as coating’s performance after accelerated weathering of short and long rotation teak for exterior utilization. In this study, the samples were heated in oven at 220 °C for 20 h under nitrogen atmosphere. Results showed that independently of growth conditions teak woods underwent hemicelluloses degradation and an increase of lignin content after heat treatment. Extractives contents were lower in short rotation than in long rotation teak, and decreased in all cases after heat treatments. Dimensional stability was considerably improved as indicated by anti-swelling efficiency values of 64.9% and 58.9% for short and long rotation teak, respectively. Heated teak woods were more resistant against Trametes versicolor and the durability of short-rotation teak increased from moderate to very durable. Coatings on heat treated teaks had better bonding quality and better photo-stability when compared to unheated. Heated short rotation teak could be considered for exterior application.