Miracle-dz/UniFAR-FTUs huggingface dataset:
Overcoming paralogy and incomplete lineage sorting to detect a phylogeographic signal: a GapC study of Armeria pungens

Low-copy nuclear genes have been suggested as a promising source of independent phylogeographic markers in plants. However, the available studies at the intraspecific level have revealed that extracting information from them is frequently hampered by paralogy and lack of coalescence of alleles. It is thus relevant to test their utility with plants for which solid data from other markers are available. The aims of this study are to retrieve phylogeographic useful information in a low-copy nuclear gene by examining the congruence of the genetic variation with the geography, as well as with previous nuclear ribosomal, plastid, and amplified fragment length polymorphism (AFLP) markers. Seven combinations of primers have been assayed to characterize the structure of GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) in Armeria pungens (Link) Hoffmanns. & Link, a linearly distributed Atlantic–Mediterranean disjunct sand-dune species. A matrix of 101 direct sequences from 71 individuals was analysed with .
MOLECULAR IDENTIFICATION OF SPONGES OBTAINED FROM SERIBU ISLANDS NATIONAL PARK AND THEIR ASSOCIATED BACTERIA

Sponges are simple multicellular animals that produced many pharmaceutical secondary metabolites. Some sponge-associated bacteria are proven to produce the same metabolites as their host, giving an opportunity to mass produce the potential metabolites. The aim of this research was to analyze the diversity of sponge-associated bacteria and to identify the host sponge. Samples were collected from Seribu Islands National Park. Partial identification of sponges were conducted by molecular technique with the mitochondrial cytochrome oxidase subunit 1 (CO1) as the target area. The diversity of sponge-associated bacteria was determined by Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. Result showed that sponges PS-17-12 has similarity with Petrosia sp. , while PS-26-12 and PS-38-12 has similarity with Xestospongia muta. From the 3 sponge samples, 85 species of bacteria was obtained which can be classified into 9 phylums and 1 uncultured bacteria/environment sample. Some of the sponge-associated bacteria identified were known as a potential producer of metabolites with antibiotic activity.
Reduction of Visual Disruptions in Coronary Cine-Angiography for Better Diagnostic Viewing

Coronary angiography is an invasive medical imaging modality which is widely used as a preliminary diagnostic method in Interventional Cardiology for detection of luminal obstructions in Coronary Arteries (CA). Noise, non-uniform illumination, low contrast and epicardial motion are considered as the reported visual degradations which are automatically recorded in Coronary angiography. Further, those factors form certain unpredictable obstructions during the angiography based disease diagnosis. In this study, it has been proposed a frequency filtering based frame enhancement method for surmounting those problems and improving the visual quality of the angiograms. The proposed method is based on homomorphic butter worth high pass filter and empirically validated contrast stretching technique. Further, the optical flow based frame stabilization method has been applied in the later stages of the proposed method for correcting the epicardial deformations. The results of the study clearly emphasized the visual improvement obtained from this method. The enhanced angiography frames produced in this study can be recommended for reliable stenosis detection. Further, these enhanced frames can be further used for quantitative stenosis assessment.
Effects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattle

Abstract Considerable evidence has demonstrated that the μ-calpain (CAPN1) gene and its inhibitor calpastatin (CAST) gene are major factors affecting meat quality. Marker-assisted selection (MAS) has been widely used to improve beef quality traits. Therefore, the objective of the present study was to investigate the single nucleotide polymorphisms (SNPs) of bovine CAPN1 and CAST genes using 367 animals representing the four main Chinese cattle breeds and to explore the effects of these SNPs on meat quality traits. Two SNPs within CAPN1 and one SNP in CAST were successfully identified in cattle. Genetic diversity analyses suggested that most SNPs in the four breeds exhibited a moderate genetic diversity. Moreover, associations between individual markers and meat quality traits were analyzed in Chinese Simmental cattle. The CAPN1 4558 A > G locus was found to be significantly associated with shear force value (SFV) and marbling score (BMS), and CAPN1 4684 C > T exerted a significant effect on SFV, while the CAST genotype was not significantly associated with any of the measured traits. SFV, commonly used to measure meat tenderness, represents an important quality trait as it contributes to the flavor of cooked meat. This work confirms the effect of CAPN1 on beef tenderness and lays an important foundation for future cattle breeding.
ALLOZYME-BASED GENETIC VARIABILITY OF THE DAPHNIA ATKINSONI-BOLIVARI SPECIES COMPLEX (CLADOCERA: DAPHNIIDAE) IN THE HUNGARIAN GREAT PLAIN

Allozyme polymorphism investigation was performed with the aim to evaluate some population genetic characteristics of two species, Daphnia atkinsoni Baird, 1859 and Daphnia bolivari Richard, 1888 (Cladocera: Daphniidae), of temporary aquatic habitats in the Hungarian Great Plain. The analysis showed that D. bolivari is not a distinct taxon, but is nested within D. atkinsoni. At the same time, remarkable within-species differentiation was revealed in D. atkinsoni; two presumable cryptic lineages were detected by our enzyme polymorphism investigation. The separation of the lineages is mainly due to the allozyme pattern at the AAT locus. Multivariate analysis of abiotic variables of the sampling sites revealed the relation between the genetic and ecological data, pH being the relevant variable explaining 81% of the genetic variability.
FUSION OF LOCATION FINGERPRINTING AND TRILATERATION BASED ON THEEXAMPLE OF DIFFERENTIAL WI-FI POSITIONING

Abstract. Positioning of mobile users in indoor environments with Wireless Fidelity (Wi-Fi) has become very popular whereby location fingerprinting and trilateration are the most commonly employed methods. In both the received signal strength (RSS) of the surrounding access points (APs) are scanned and used to estimate the user’s position. Within the scope of this study the advantageous qualities of both methods are identified and selected to benefit their combination. By a fusion of these technologies a higher performance for Wi-Fi positioning is achievable. For that purpose, a novel approach based on the well-known Differential GPS (DGPS) principle of operation is developed and applied. This approach for user localization and tracking is termed Differential Wi-Fi (DWi-Fi) by analogy with DGPS. From reference stations deployed in the area of interest differential measurement corrections are derived and applied at the mobile user side. Hence, range or coordinate corrections can be estimated from a network of reference station observations as it is done in common CORS GNSS networks. A low-cost realization with Raspberry Pi units is employed for these reference stations. These units serve at the same time as APs broadcasting Wi-Fi signals as well as reference stations scanning the receivable Wi-Fi signals of the surrounding APs. As the RSS measurements are carried out continuously at the reference stations dynamically changing maps of RSS distributions, so-called radio maps, are derived. Similar as in location fingerprinting this radio maps represent the RSS fingerprints at certain locations. From the areal modelling of the correction parameters in combination with the dynamically updated radio maps the location of the user can be estimated in real-time. The novel approach is presented and its performance demonstrated in this paper.
Autonomous navigation of a UAV based on multimodal integration

While most of the UAV mission scenarios considered in the literature inherently need the robot to combine multiple and often conflicting objectives, in practice, most of systems finally decompose the problem by switching between exclusive behaviors, i.e. controllers. As an example, the Paparazzi system developed at ENAC [1] provides autonomous flight plan execution by statically selecting the appropriate controller according to the current objective.
A correlational analysis of human cognitive activity using Infrared Thermography of the supraorbital region, frontal EEG and self-report of core affective state.

Using Infrared Thermography, three-way statistical correlation between forehead temperatures, frontal EEG and self-reports of core affect was applied in an experimental study to establish the underlying causal relationships between cognitive activity and supraorbital blood flow. Sub-groups were identified within the sample using the differentia of tonic forehead temperature asymmetry. Comparison between these groups showed that the so-called Right Dominant temperature sample exhibited statistically significant correlations between asymmetry in frontal alpha, forehead temperature and self-reported arousal throughout the experimental interactions. Individuals exhibiting this trait demonstrated greater reactivity to variation in the cognitive challenge of the tasks, presenting more readily measurable and distinctive patterns of asymmetric frontal cortical activity and temperature change. Detailed analysis showed significant patterns of correlation between hemispherical changes in specific beta frequencies, forehead temperature and self reported arousal and task engagement, indicating that forehead temperature dynamics reflected the underlying variation in cognitive demand evoked by the experimental stimuli.
Comparison of the validation of two analytical methods for fungal toxins according to RELACRE and the European Decision 2002/657/EC Análise comparativa de dois métodos para análise de micotoxinas de acordo com a RELACRE e a Decisão 2002/657/CE

The purpose of the present paper is to present a comparison between the notions introduced in the 2002/657/EC European Decision and the concepts already established by RELACRE (association of the accredited laboratories of Portugal), with respect to in-house validation of analytical methods based on HPLC. The comparison is applied and discussed for the in-house validation of deoxynivalenol (DON) and zearalenone (ZEN) analysis, according to two different methodologies. The parameters validated in accordance with the 2002/657/EC European Decision were specificity, linearity, sensitivity, decision limit (CCα), detection capability (CCβ), repeatability, recovery and ruggedness. To satisfy this protocol minimal assays number appears to be 99, for quantitative and confirmatory methods. Several concentration ranges were tested, calibration curves and their respective linearity were established. Values for analytical parameter values and methods performance were determined. The observed detection and quantification limits (DL and QL) were: 32 µg/kg and 96 µg/kg, for DON and 34 µg/kg and 104 µg/kg for ZEN. CCα values were 190 µg DON /kg and 57 µg ZEN/kg. CCβ values were 277 µg DON /kg and 77 µg ZEN/kg.
Time-lapse slip variation associated with a medium-size earthquake revealed by

Abstract. We obtained the time-lapse cumulative slip before and after the 29 November 1999, Xiuyan, Liaoning, China, Ms = 5.4 earthquake by using "repeating events" defined by waveform cross-correlation. We used the seismic waveform data from the Liaoning Regional Seismograph Network from June 1999 to December 2006. Two "multiplets" located near the seismogenic fault of the 1999 Xiuyan earthquake and the 4 February 1975, Haicheng Ms = 7.3 earthquake, respectively, were investigated. For the "multiplet" that occurred before and after the 1999 Xiuyan earthquake, apparent pre-shock accelerating-like slip behavior, clear immediate-post-seismic change, and relaxation-like post-seismic change can be observed. As a comparison, for the "multiplet" near the 1975 Haicheng earthquake which occurred a quarter century ago, the cumulative slip appears linear with a much smaller slip rate.
Visible and near infrared spectroscopy for predicting texture in forest soil: an application in southern Italy

Abstract: Texture is a primary variable affecting the total amount of carbon stock in the soil. The standard methods for determining soil texture, however, are still conducted manually and are largely time-consuming. Reflectance spectroscopy in the visible, near infrared (Vis-NIR, 350-2500 nm) spectral region could be an alternative to standard laboratory methods. The aim of this paper was to develop calibration models based on laboratory Vis-NIR spectroscopy and PLSR analysis to estimate the texture (sand: 2-0.05 mm; silt: 0.05-0.002 mm; clay: <0.002 mm) in a forest area of southern Italy. An additional objective was to produce continuous maps of sand, silt and clay through a geostatistical approach. Soil samples were collected at 235 locations in the study area, and then dried, sieved at 2 mm and analyzed in laboratory for soil texture and Vis-NIR spectroscopic measurements. Spectra showed that soil samples could be spectrally separable on the basis of classes of texture. To establish the relationships between spectral reflectance and soil texture (sand, silt and clay) partial least squared regression (PLSR) analysis was applied to 175 soil samples, while the remaining 60 samples were used to validate the models. The optimum number of factors to be retained in the calibration models was determined by leave-one-out cross-validation. Results of cross validation of calibration models indicated that the models fitted quite well and the values of R2 ranged between a minimum value of 0.74% for silt and a maximum value of 0.84 for sand content. Results for validation were satisfactory for sand content (R2=0.81) and clay content (R2=0.80) and less satisfactory for silt content (R2=0.70). Geostatistics coupled with Vis-NIR reflectance spectroscopy allowed us to produce continuous maps of sand, silt and clay, which are of critical importance for understanding and managing forest soils.
Cytotoxic Effects of Drug-loaded Hyaluronan-Glutaraldehyde Cross-Linked Nanoparticles and the Release Kinetics Modeling

In this study, paclitaxel (PTX)-loaded hyaluronic acid (HA) nanoparticles (NPs) were synthesized. FESEM and TEM showed HA-PTX NPs with spherical shape and sizes >100 nm. TheHA entrapment maintained the crystalline nature of PTX as suggested by XRD, and the entrapment was confirmed by the characteristic peak of PTX at 1736 cm-1 by FTIR. HA-PTX showed cytotoxicity towards lung (A549) (IC50 0.3 μg/ml), breast (MCF-7) (IC500.2 μg/ml) and colorectal (HT-29) (IC50 0.2 μg/ml) cancer cells, with 2-3 fold more cytotoxic effects than free PTX. At 10 ng/ml in A549 cell lines, PTX induced apoptosis, whilst HA-PTX showed enhanced apoptosis. The release kinetics profile showed PTX release in a biphasic manner, with initial burst release of 60-70%, followed by a slow and uniform release. PTX release was best modeled by first-order kinetics, Higuchi and Korsmeyer-Peppas models suggesting that it was concentration dependent, with anomalous, non-Fickian diffusion as a predominant mechanism for the drug transport.
A Mathematical Model of Flavescence Dorée

7 Flavescence dorée (FD) is a disease of grapevine transmitted by an insect vector, Scaphoideus titanus Ball. At present, no prophylaxis exists, so mandatory control procedures (e.g. removal of infected plants, and insecticidal sprays to avoid transmission) are in place in Italy and other European countries. We propose a model of the epidemiology of FD by taking into account the di erent aspects involved into the transmission process (acquisition of the disease, latency and expression of symptoms, recovery rate, removal and replacement of infected plants, insecticidal treatments, and the e ect of hotbeds). The model was constructed as a system of rst order nonlinear ODEs in four compartment variables. A bifurcation analysis shows that, in the absence of hotbeds, the state of healthy vineyard is stable, if removal and replacement of infected plants is implemented. In the presence of hotbeds, depending on the grapevine density, we nd either a single family of equilibria in which the health of the vineyard gradually deteriorates for progressively more severe hotbeds, or multiple equilibria that give rise to sudden transitions from a nearly healthy vineyard to a highly deteriorated one when the severity of the hotbeds crosses a critical value. These results show the long-term risks in planting new vineyards in environmental situations where strong hotbeds of FD are present or may arise in the surroundings. ∗Corresponding author ∗∗Principal corresponding author Email addresses: federico.lessio@unito.it (Federico Lessio), alessandro.portaluri@unito.it (Alessandro Portaluri), francesco.paparella@unisalento.it (Francesco Paparella), alberto.alma@unito.it (Alberto Alma) Preprint submitted to Elsevier May 15, 2015
Observation, modeling and interpretation of the star forming region S140

We investigate the influence of external and internal high-energy radiation on the chemical network in the star forming region S140 with the chemical model by Stauber et al. (2005). Rotational transitions of CN, CS, HCN, HNC, HCO+, H13CO+, DCO+, SO, H2CO and 13CO were observed with the KOSMA telescope. At the position of the embedded IRS cluster all transitions were detected, at five other positions the transitions with high critical densities were not or only just detectable. The density and temperature model by van der Tak et al. (2000) was extended and adjusted to fit one-dimensional radiative transfer calculations to our observations at the center position. We find that to reproduce the measured line strengths and ratios it is necessary to include a region of high density, i. e. an approximation of a clumpy structure, in the outer part of the KOSMA beam. Deeper inside the cloud, both a homogeneous model and a clump model can reproduce our observations. The results indicate that internal X-ray and FUV radiation cannot be traced in the KOSMA beam. The influence of the external FUV radiation highly depends on the clump size and the volume filling factor, both of which are not yet well constrained. The best fit of the cosmic ray ionization rate to our observations results in a value of ζ = 1 · 10−17 s−1 at the center and ζ = 7 · 10−18 s−1 at the second position. An analytic estimation from the DCO+/HCO+ ratio using a steady-state model provides a value of ζ = 1 · 10−16 s−1 if the emission is assumed to come only from the clump.
A Hybrid Control Method for Stable Operation of Active Power Filters in Three-Phase Four-Wire Networks

The main goal of this study is the use of Lyapunov’s stability theory to a three-phase four-wire shunt active power filter (SAPF), since this method has been applied effectively to other areas of converter. The dynamic model of the SAPF is first established, after that, a combination of fuzzy tracking control and Lyapunov function is suggested in order to impose a desired transient waveform on the considered three-phase four-wire distribution grid, providing robustness and insensitivity to parameter changes. Furthermore, the suggested control technique guarantees appropriate tracking of the reference current components and simplifies the global control design. The feasibility of the suggested control method is validated using comprehensive simulation studies on a four-wire SAPF in order to compensate for nonlinear and unbalanced grid-connected loads in an electrical power distribution network.
Performance on SOA Based Wavelength Conversion at 10 GB/s by dual pump four wave mixing over a 50 nm

We demonstrate an 50 nm wavelength shift using two orthogonally polarized pump with four wave mixing . We show that the wavelength conversion using of a four wave mixing in SOA ,increases the error free conversion . 50 nm wavelength down conversion 35nm up conversion have been obtained at10 Gb/s. This results a significance improvement over the previous best performance of an Fwm based wavelength converter and demonstrate the large wavelength shift capacity of Fwm technique.
Entropy in the interior of a Kerr black hole

Christodoulou et al have shown that the interior volume of a Schwarzschild black hole grows linearly with time. Subsequently, their conclusion has been extended to the Reissner–Nordström (RN) and Kerr black holes. Meanwhile, the entropy of the scalar field inside a Schwarzschild black hole has also been calculated. In this paper, a general method calculating the number of quantum states of the scalar field inside the black hole is given, which can be used in an arbitrary black hole. After introducing the two important assumptions as the black-body radiation assumption and the quasi-static process assumption, the entropy of the scalar field inside a Kerr black hole is calculated using the differential form, and we find that the variation of the entropy is proportional to the variation of the Bekenstein–Hawking entropy except the ending of the black hole evaporation. Similarly, we recalculate the entropy of the scalar field inside a Schwarzschild black hole and demonstrate that the entropy inside a Kerr black hole can exactly degenerate to the Schwarzschild black hole. As well as, we find that the proportionality coefficient between the entropy of the scalar field and the Bekenstein–Hawking entropy in Schwarzschild case, which is obtained using the differential form, is half of that given in the previous literature. Furthermore, we investigate the total entropy of Kerr and Schwarzschild black holes and find that they all increase with time. It means that the black holes, evolution with Hawking radiation satisfies the second law of thermodynamics. Finally, the black hole information paradox is brought up again and discussed.
SY 08 . 03 | Image Analysis II AUTOMATED KI 67 HOTSPOT DETECTION FOR BREAST CANCER BIOPSIES

Methods The proposed method has been tested on one Ki67 stained image from Openslide [1] acquired at 40x with an Hamamatsu scanner and on 5 Ki67 stained images of breast cancer biopsies acquired at 40x with AperioCS. Each input image is divided in tiles, whose colors are deconvolved using the method of Ruifrok [2] to estimate the presence of Ki67. Tiles with an estimated Diaminobenzidine (DAB) positivity of more than 5% are considered as potential hotspots. Neighbouring positive tiles are merged to form a final hotspot area. The three hotspot areas with higher DAB positivity are also highlighted in the output. The hotspot areas are then written in an XML file which is read by a medical image viewer such as Aperio ImageScope. The proposed method has been implemented in Java using the BioFormats open source library [3].