Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Relationships and Classification of Several Tufted Capuchin Lineages (Cebus apella, Cebus xanthosternos and Cebus nigritus, Cebidae), by Means of Mitochondrial Cytochrome Oxidase II Gene Sequences

The morphological systematics of the tufted capuchins is confusing. In an attempt to clarify the complex systematics and phylogeography of this taxon, we provide a first molecular analysis. We obtained mitochondrial cytochrome oxidase II (mtCOII) gene sequences from 49 tufted capuchins that had exact geographic origins from diverse lineages in Colombia, Peru, Bolivia, French Guyana, Brazil, Argentina and Paraguay and that belonged to clearly recognized morphological taxa. This project had 4 main findings: (1) we determined 2 established and related taxa in the northern Amazon River area, which we named C. a. apella and C. a. fatuellus. C. a. apella is distributed from French Guyana until, at least, the Negro River in the northern Brazilian Amazon, whereas C. a. fatuellus is distributed throughout the Colombian Eastern Llanos and the northern Colombian Amazon. We also determined 2 other southern C. apella taxa, which we named C. a. macrodon and C. a. cay. C. a. macrodon has a western and southern Amazon distribution, while C. a. cay has a more southern distribution outside the Amazon basin. (2) In the upper Amazon basin, there is a unique lineage (C. a. macrocephalus) with 1 widely distributed haplotype. The 4 morphological subspecies (C. a. maranonis, C. a. macrocephalus, C. a. peruanus, C. a. pallidus), and maybe a fifth unknown subspecies, described in this area were molecularly undifferentiated at least for the mitochondrial gene analyzed. (3) Our molecular analysis determined that 1 individual of C. robustus fell into the lineage of C. a. macrocephalus. Therefore, this form does not receive any specific name. (4) The animals classified a priori as C. nigritus and C. xanthosternos (because of their morphological phenotypes and by their geographical origins) were clearly differentiated from the other specimens analyzed with the molecular marker employed. Therefore, we consider that these 2 lineages could be assigned the status of full species following the biological species definition. (5) In 2001, Groves described 4 tufted capuchin species (C. apella, C. libidinosus, C. nigritus and C. xanthosternos), while Silva Jr. determined 7 species (C. apella, C. macrocephalus, C. libidinosus, C. cay, C. nigritus, C. robustus and C. xanthosternos). The tests of Swofford-Olsen-Waddell-Hillis, of Shimodaira and Hasegawa and of Templeton did not fit with either of these two classificatory schemes, although Groves’ scheme was better with regard to our data than that of Silva Jr. (6) All the temporal splits among the tufted capuchin taxa studied were estimated to have occurred during the last phase of the Pleistocene by using the ρ statistic applied to the median joining haplotype network.
Transplantation of alginate microcapsules: generation of antibodies against alginates and encapsulated porcine islet-like cell clusters.

BACKGROUND Microencapsulation of islets of Langherhans in alginate poly-L-lysine capsules provides an effective protection against cell-mediated immune destruction, and ideally should allow the transplantation of islets in the absence of immunosuppression. It has previously been suggested that alginate rich in mannuronic acid (high M) is more immunogenic than alginate rich in guluronic acid (high G). The ability of these alginates to induce an antibody response in the recipient or act as an adjuvant to antibody responses against antigens leaked from the capsule was investigated in the present study. METHODS Empty capsules made from these different types of alginate were transplanted intraperitoneally to Wistar rats or Balb/c mice. In addition, some animals were also injected with bovine serum albumin to assess the ability of the alginates to act as an adjuvant to this antigen. Antibody responses to intraperitoneally transplanted free and microencapsulated fetal porcine islet like cell clusters (ICC) were also evaluated, in animals treated with or without cyclosporine. RESULTS Antibodies against high M-alginate capsules were detected in the sera of mice transplanted with this capsule type. However, this response was not seen after the transplantation of high G capsules. When Wistar rats were used as recipients, no antibody responses were detected against any type of alginate capsules. Neither type of capsule acted as an adjuvant. Antibodies against ICC were present, in rats transplanted with both nonencapsulated and encapsulated ICCs. Administration of cyclosporine could abolish this production of antibodies against ICC. CONCLUSIONS High G-alginate capsules are less immunogenic than high M capsules. Because encapsulation did not protect against the generation of antibodies against ICC, it can be assumed that antigen leakage from the capsules occurs, as no evidence was found for capsules breaking in vivo.
Simulation of an oil film at the sea surface and its radiometric properties in the SWIR

The knowledge of the optical contrast of an oil layer on the sea under various surface roughness conditions is of great interest for oil slick monitoring techniques. This paper presents a 3D simulation of a dynamic sea surface contaminated by a floating oil film. The simulation considers the damping influence of oil on the ocean waves and its physical properties. It calculates the radiance contrast of the sea surface polluted by the oil film in relation to a clean sea surface for the SWIR spectral band. Our computer simulation combines the 3D simulation of a maritime scene (open clear sea/clear sky) with an oil film at the sea surface. The basic geometry of a clean sea surface is modeled by a composition of smooth wind driven gravity waves. Oil on the sea surface attenuates the capillary and short gravity waves modulating the wave power density spectrum of these waves. The radiance of the maritime scene is calculated in the SWIR spectral band with the emitted sea surface radiance and the specularly reflected sky radiance as components. Wave hiding and shadowing, especially occurring at low viewing angles, are considered. The specular reflection of the sky radiance at the clean sea surface is modeled by an analytical statistical bidirectional reflectance distribution function (BRDF) of the sea surface. For oil at the sea surface, a specific BRDF is used influenced by the reduced surface roughness, i.e., the modulated wave density spectrum. The radiance contrast of an oil film in relation to the clean sea surface is calculated for different viewing angles, wind speeds, and oil types characterized by their specific physical properties.
Validation of deconvolution analysis of LH secretion and half-life.

Deconvolution methods constitute a class of analytic tools to quantitate hormone secretion and/or clearance in vivo. Although mathematically rigorous, deconvolution techniques have assumed, rather than proven, validity. Accordingly, we tested the validity of deconvolution analysis on true-positive human, animal (sheep and monkey), and computer-simulated data using the luteinizing hormone (LH) pulse signal as a relevant paradigm. We found that multiparameter deconvolution analysis has high discriminative sensitivity (human data 91%, animal 81%, computer-stimulated 95%) and specificity (human 90%, animal 81%, computer-simulated 100%). Sensitivity was impaired by low secretory burst amplitude (< 0.1 IU.l-1.min-1), short interpulse interval (< 60 min), infrequent venous sampling (every 20-30 min), and high random experimental variation (e.g., noise > 15%). Specificity was hindered by noise. Deconvolution accurately characterized the unknown hormone half-life (r = +0.994) and production rate (r = +0.990). Interoperator reliability was high when statistically based criteria for secretory pulse detection were applied. We conclude that multiparameter deconvolution, within recognizable constraints, is a valid and reliable tool for in vivo investigation of hormone secretion and half-life.
Acoustic data-driven grapheme-to-phoneme conversion using KL-HMM

This paper proposes a novel grapheme-to-phoneme (G2P) conversion approach where first the probabilistic relation between graphemes and phonemes is captured from acoustic data using Kullback-Leibler divergence based hidden Markov model (KL-HMM) system. Then, through a simple decoding framework the information in this probabilistic relation is integrated with the sequence information in the orthographic transcription of the word to infer the phoneme sequence. One of the main application of the proposed G2P approach is in the area of low linguistic resource based automatic speech recognition or text-to-speech systems. We demonstrate this potential through a simulation study where linguistic resources from one domain is used to create linguistic resources for a different domain.
Enhancements in robust feature matching

We present in this paper a number of new enhancements to a branch-and-bound algorithm given by Mount, Netanyahu, and Le Moigne [8] for feature matching. We introduce a new distance measure, which is more robust to the presence of outliers than the previously used measure, as well as a new variant of the search algorithm and a new search strategy. We also present experimental results, which show that these enhancements offer significant tangible improvements in performance.
Genetic factors conferring an increased susceptibility to develop Crohn's disease also influence disease phenotype: results from the IBDchip European Project

Objective Through genome-wide association scans and meta-analyses thereof, over 70 genetic loci (Crohn's disease (CD) single nucleotide polymorphisms (SNPs)) are significantly associated with CD. We aimed to investigate the influence of CD-SNPs and basic patient characteristics on CD clinical course, and develop statistical models to predict CD clinical course. Design This retrospective study included 1528 patients with CD with more than 10 years of follow-up from eight European referral hospitals. CD outcomes of interest were ileal (L1), colonic (L2) and ileocolonic disease location (L3); stenosing (B2) or penetrating behaviour (B3); perianal disease; extraintestinal manifestations; and bowel resection. A complicated disease course was defined as stenosing or penetrating behaviour, perianal disease and/or bowel resection. Association between CD-SNPs or patient characteristics and specified outcomes was studied. Results Several CD-SNPs and clinical characteristics were statistically associated with outcomes of interest. The NOD2 gene was the most important genetic factor, being an independent predictive factor for ileal location (p=2.02×10-06, OR=1.90), stenosing (p=3.16×10-06, OR=1.82) and penetrating (p=1.26×10-02, OR=1.25) CD behaviours, and need for surgery (p=2.28×e-05, OR=1.73), and as such was also the strongest factor associated with a complicated disease course (p=6.86×10-06, OR=2.96). Immunomodulator (azathioprine/6-mercaptopurine and methotrexate) use within 3 years after diagnosis led to a reduction in bowel stenoses (p=1.48×10-06, OR=0.35) and surgical rate (p=1.71×10-07, OR=0.34). Association between each outcome and genetic scores, created using significant SNPs in the univariate analysis, revealed large differences in the probability of developing fistulising disease (IL23R, LOC441108, PRDM1, NOD2; p=9.64e-4, HR=1.43), need for surgery (IRGM, TNFSF15, C13ORF31, NOD2; p=7.12×10-03, HR=1.35), and stenosing disease (NOD2, JAK2, ATG16L1; p=3.01×10-02, HR=1.29) among patients with low and high score. Conclusions This large multicentre cohort study has found several genetic and clinical factors influencing the clinical course of CD. NOD2 and early immunomodulator use are the clinically most meaningful predictors for its clinical course.
Outcome after treatment of congenital unilateral cataract.

PURPOSE To evaluate long-term functional outcome after treatment of congenital unilateral cataract. METHODS The records of 30 consecutive children operated on before the age of 12 months at St. Erik's Eye Hospital over a 5-year period (1991-96) were reviewed retrospectively. The patients were followed until 4-9.5 years of age. Linear Snellen visual acuity (VA), occlusion therapy compliance, and the presence of nystagmus, strabismus and other complications are reported. RESULTS Six children achieved VA of 0.1 or better. They were all operated on before 3 months of age. Of the 12 infants operated on before 6 weeks of age, four have VA between 0.3 and 0.4 and eight have VA of finger counting or less. Four developed severe secondary glaucoma within 6 months of cataract extraction. Two of these had persistent fetal vasculature. Three eyes developing glaucoma became amaurotic. Occlusion therapy was abandoned before the age of 2.5 years in 21 children. CONCLUSION Good levels of VA were achieved only in children who underwent cataract surgery before 3 months of age and who adhered to the occlusion therapy schedule. Severe secondary glaucoma developed in four out of 12 children operated on within 6 weeks. Full compliance with the occlusion therapy programme was uncommon.
Visual Narrative Flow: Exploring Factors Shaping Data Visualization Story Reading Experiences

Many factors can shape the flow of visual data‐driven stories, and thereby the way readers experience those stories. Through the analysis of 80 existing stories found on popular websites, we systematically investigate and identify seven characteristics of these stories, which we name “flow‐factors,” and we illustrate how they feed into the broader concept of “visual narrative flow. ” These flow‐factors are navigation input, level of control, navigation progress, story layout, role of visualization, story progression, and navigation feedback. We also describe a series of studies we conducted, which shed initial light on how different visual narrative flows impact the reading experience. We report on two exploratory studies, in which we gathered reactions and preferences of readers for stepper‐ vs. scroller‐driven flows. We then report on a crowdsourced study with 240 participants, in which we explore the effect of the combination of different flow‐factors on readers’ engagement. Our results indicate that visuals and navigation feedback (e.g., static vs. animated transitions) have an impact on readers’ engagement, while level of control (e.g., discrete vs. continuous) may not.
Untainted Puncturing for Irregular Low-Density Parity-Check Codes

Puncturing is a well-known coding technique widely used for constructing rate-compatible codes. In this paper, we consider the problem of puncturing low-density parity-check codes and propose a new algorithm for intentional puncturing. The algorithm is based on the puncturing of untainted symbols, i.e. nodes with no punctured symbols within their neighboring set. It is shown that the algorithm proposed here performs better than previous proposals for a range of coding rates and short proportions of punctured symbols.
Fagus sylvatica forest vegetation in Greece: Syntaxonomy and gradient analysis

This is the first comprehensive study on Fagus sylvatica s.l. forest communities in Greece. It is based on the multivariate analysis of more than 1100 releves throughout the distribution area of Fagus in Greece, 60 % of which have been sampled within the last 15 years. The data were compiled from all relevant literature and from unpublished field studies. Prior to data analysis, taxonomic and floristic inaccuracies in older literature have been corrected, and some taxa aggregated. Status and distribution of Fagus in Greece, as well as histori- cal and silvicultural aspects, are outlined. Classification re- sulted in 16 vegetation types defined by species composition, of which 10 units are ranked as association (of which two were described as new) or community, with six subcommunities included. Synonyms from the literature are given to all types. The floristic structure of the data set is displayed by a synoptic table and by DCA ordination. Community differentiation fol- lows a complex edaphic-climatic-phytogeographic pattern. Apart from Fagus sylvatica ssp. orientalis forests of warm and dry habitats and low to medium altitudes which are related to deciduous Quercus forests, four Fagion community groups are distinguished which represent different habitat types: (1) cool, humid, mesotrophic; (2) cool, acidic; (3) high altitude, calcareous; (4) medium altitude, moderately warm and dry. The communities may be assigned to three regional sub- alliances, viz. (a) Doronico orientalis-Fagenion at medium altitudes of North-Central and East-Central Greece; (b) Doronico columnae-Fagenion in the far north and at high altitudes southward to East-Central Greece; (c) Geranio striati- Fagenion in the Northwest. Various types of thermophilous beech forest are assigned to (a) and (c), acidic forest to (b), and mesic Fagus forest to (b) and (c).
Modelling and Simulation of Hypoxia Imaging with Positron Emission Tomography

Hypoxia can be assessed non-invasively by positron emission tomography (PET) using radiotracers such as [18F]fluoromisonidazole (Fmiso) accumulating in poorly oxygenated cells. Typical features of dynamic Fmiso PET data are high signal variability in the first hour after tracer administration and slow formation of a consistent contrast. The purpose of this study is to investigate whether these characteristics can be explained by the current conception of the underlying microscopic processes and to identify fundamental effects. This is achieved by modelling and simulating tissue oxygenation and tracer dynamics on the microscopic scale. In simulations, vessel structures on histology-derived maps act as sources and sinks for oxygen as well as tracer molecules. Molecular distributions in the extravascular space are determined by reaction–diffusion equations, which are solved numerically using a twodimensional finite element method. Simulated Fmiso time activity curves (TACs), though not directly comparable to PET TACs, reproduce major characteristics of clinical curves, indicating that the microscopic model and the parameter values are adequate. Evidence for dependence of the early PET signal on the vascular fraction is found. Further, possible effects leading to late contrast formation and potential implications on the quantification of Fmiso PET data are discussed. (Some figures in this article are in colour only in the electronic version) 0031-9155/11/072045+13$33.00 © 2011 Institute of Physics and Engineering in Medicine Printed in the UK 2045 2046 D Mönnich et al
On incomplete symmetric orthogonal polynomials of Jacobi type

In this paper, by using the extended Sturm–Liouville theorem for symmetric functions, we introduce the following differential equation in which β=−2s(2s+2a−2m+1), γ=2s(2s+2a−2m+1)−2(2r+1)(r+a−m+1) and α n =(mn+2s+(r−s+(m−1)/2)(1−(−1) n ))(mn+2s+2a+1+2mb+(r−s+(m−1)/2)(1−(−1) n )) and show that one of its basic solutions is a class of incomplete symmetric polynomials orthogonal with respect to the weight function |x|2a (1−x 2m ) b on [−1,1]. We also obtain the norm square value of this orthogonal class.
Single Stage High Frequency LC Resonant Inverter

High power factor, high frequency single stage single switch resonant inverter for the application of high frequency applications is presented in this paper. The power circuit is designed with a power factor corrector with single-switch current-fed high frequency resonant inverter. Number of switches used in conventional ballast circuits is reduced in single switch approach. SEPIC (Single ended primary inductor converter) is operated in DCM (discontinuous conduction mode) and the drawbacks of conventional class E resonant are overcome. The problem of gate circuit design of switches and isolation are greatly reduced due to the usage of single switch. The presence of input filters makes the input current ripple free. The simulation results of single switch High Frequency Resonant Inverter for CFL Applications circuit for high frequency of 80 kHz have been presented.
Utilização de máquina de vetor de suporte para previsão de níveis de água subterrânea

This work had a purpose to use a regression technique with Support Vector Machine (SVM) to predict daily water-table levels of groundwater in a monitoring well on unconfined aquifer in the west of Rio Grande do Sul. For that, was used time series of static water level and rainfall, comprising daily monitoring period of 1468 observations. The aim was to create an autoregressive model capable of estimate groundwater levels from the time series for horizons of 120 and 180 days. At the test step of the model, the adjustment of prediction realized presented statistical coefficients (R²) of 0,89 and Nash-Sutcliffe coefficients (CNS) of 0,90, attesting the predictive quality of the methodology used. After the analysis of the residues, it was verified greater efficiency for the prediction of discharge events, mainly, for high static water levels. The use of present methodology showed high accuracy to estimate the groundwater level using only the static water level and rainfall variables, demonstrating great applicability in groundwater hydrology field.
EEG features of absence seizures in idiopathic generalized epilepsy: Impact of syndrome, age, and state

Purpose: Factors influencing the electroencephalography (EEG) features of absence seizures in newly presenting children with idiopathic generalized epilepsy (IGE) have not been rigorously studied. We examined how specific factors such as state, provocation, age, and epilepsy syndrome affect the EEG features of absence seizures.
Learning Filter Banks Using Deep Learning For Acoustic Signals

Designing appropriate features for acoustic event recognition tasks is an active field of research. Expressive features should both improve the performance of the tasks and also be interpret-able. Currently, heuristically designed features based on the domain knowledge requires tremendous effort in hand-crafting, while features extracted through deep network are difficult for human to interpret. In this work, we explore the experience guided learning method for designing acoustic features. This is a novel hybrid approach combining both domain knowledge and purely data driven feature designing. Based on the procedure of log Mel-filter banks, we design a filter bank learning layer. We concatenate this layer with a convolutional neural network (CNN) model. After training the network, the weight of the filter bank learning layer is extracted to facilitate the design of acoustic features. We smooth the trained weight of the learning layer and re-initialize it in filter bank learning layer as audio feature extractor. For the environmental sound recognition task based on the Urban- sound8K dataset, the experience guided learning leads to a 2% accuracy improvement compared with the fixed feature extractors (the log Mel-filter bank). The shape of the new filter banks are visualized and explained to prove the effectiveness of the feature design process.
Fast Trace Generation of Many-Core Embedded Systems with Native Simulation

Embedded Software development and optimization are complex tasks. Late availably of hardware platforms, their usual low visibility and controllability, and their limiting resource constraints makes early performance estimation an attractive option instead of using the final execution platform. With early performance estimation, software development can progress although the real hardware is not yet available or it is too complex to interact with. In this paper, we present how the native simulation framework SCoPE is extended to generate OTF trace files. Those trace files can be later visualized with trace visualization tools, which recently were only used to optimize HPC workloads in order to iterate in the development process.