Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of specific primers for the detection of HVA1 from barley in transgenic durum wheat by polymerase chain reaction (PCR) technology

Genetic transformation is a widely employed tool in both basic research and commercial plant breeding programs. Its application requires that transgenes be stably integrated and expressed in the plant genome. When transgenic plants are developed, it is essential to determine which plants contain the transgene. Detection methods are usually based on amplification of the target transgene. This paper describes a development of detection method based on conventional and real time polymerase chain reaction (PCR) for simultaneous detection of barley HVA1 transgene and its transcript in transformed durum wheat. Since there exist a high homology between the barley HVA1 gene and the wheat gene, development of a specific sets of primers is needed for PCR-based characterizations, and the study of the transgene. Based on the alignment of the two genes sequences obtained from public databases, several primers were designed to detect and distinguish between the transformed and non-transformed plants. Real time PCR has been employed because of its inherent sensitivity and quantitative nature. It has been possible to design the following primers pairs F2/MMR, F2/R10 and F14/R10 as highly specific and suitable for the detection of HVA1 DNA by conventional and real-time PCR. Nonetheless, the primers used were allowed to reach high efficiencies and did not show any cross-reactivity with DNAs extracted from various plants. The sensitivity achieved was 6.4 pg. The primer pair F2/R10 was considered as highly specific for the detection of both DNA and mRNA of the HVA1 by real-time PCR. The assays proved to be accurate, specific, sensitive and sufficiently reproducible for further application in high-throughput molecular characterization of transgenic lines. Key words: HVA1, durum wheat, transgenic plant, real time polymerase chain reaction (PCR), drought.
Cellulose Grafting by Atom Transfer Radical Polymerization Method

Increased public awareness on environmental issues, fluctuations in raw material prices, and global difficulties in raw material supplies have made it necessary to find new, sustainable, environment-friendly, and inexpensive natural polymer sources. Cellulose and its derivatives, at this point, have become an important research matter once again, because of its easy accessibility, abundance, price, minimal effect on the environment, and new properties discovered with the help of technology. This study explains cellulose and its modification, and gives information about ATRP, which is a controlled radical polymerization. Later, detailed information on grafting of cellulose by ATRP in both, the author’s studies and other existing researches is provided. chloride with a 21.3% yield by mole. The vinyl monomers such as 4NPA, NCA, 4VP, AM, MAM, DAAM, and MMA were grafted into the cellulose methacrylate via free-radical polymerization using 2,2'-azobis (isobutyronitrile) as an initiator in acetonitrile. The graft copolymers were characterized by FT-IR spectra, elemental
Origination and extinction components of taxonomic diversity: general problems

Abstract Mathematical modeling of cladogenesis and fossil preservation is used to explore the expected behavior of commonly used measures of taxonomic diversity and taxonomic rates with respect to interval length, quality of preservation, position of interval in a stratigraphic succession, and taxonomic rates themselves. Particular attention is focused on the independent estimation of origination and extinction rates. Modeling supports intuitive and empirical arguments that single-interval taxa, being especially sensitive to variation in preservation and interval length, produce many undesirable distortions of the fossil record. It may generally be preferable to base diversity and rate measures on estimated numbers of taxa extant at single points in time rather than to adjust conventional interval-based measures by discarding single-interval taxa. A combination of modeling and empirical analysis of fossil genera supports two major trends in marine animal evolution. (1) The Phanerozoic decline in taxonomic rates is unlikely to be an artifact of secular improvement in the quality of the fossil record, a point that has been argued before on different grounds. (2) The post-Paleozoic rise in diversity may be exaggerated by the essentially complete knowledge of the living fauna, but this bias is not the principal cause of the pattern. The pattern may partly reflect a secular increase in preservation nevertheless. Apparent temporal variation in taxonomic rates can be produced artificially by variation in preservation rate. Some empirical arguments suggest, however, that much of the short-term variation in taxonomic rates observed in the fossil record is real. (1) For marine animals as a whole, the quality of the fossil record of a higher taxon is not a good predictor of its apparent variability in taxonomic rates. (2) For a sample data set covering a cross-section of higher taxa in the Ordovician, most of the apparent variation in origination and extinction rates is not statistically attributable to independently measured variation in preservation rates. (3) Previous work has shown that standardized sampling to remove effects of variable preservation and sampling yields abundant temporal variation in estimated taxonomic rates. While modeling suggests which rate measures are likely to be most accurate in principle, the question of how best to capture true variation in taxonomic rates remains open.
Machine learning band gap and alignment of nitride semiconductors

Nitride has been drawing much attention for nearly half a century for its wide applications in optoelectronic devices and still remains a plenty of room for materials design and discovery. Here, a large set of nitrides have been designed, with their band gap and alignment being studied by first principle calculations combined with machine learning. First, a small subset of designed nitrides were randomly selected and their band gap, band offset against wurtzite GaN were accurately calculated by HSE. Second, an 18-dimensional feature space was built upon elemental properties and HSE calculation results were used to train and test machine learning models. After comparison among the performance of support vector regression (SVR) with different kernels, linear regression and neural network (NN) with different number of hidden layers, it was found that SVR with radial kernel is the best model for predicting both band gap and band offset with prediction root mean square error (RMSE) of 0.298 eV and 0.130 eV, respectively, both of which are within HSE calculation uncertainty. Third, when band gap calculated by PBE was added into the feature space, band gap prediction RMSE decreases to 0.099 eV. Through a feature engineering, elemental-property-based recursive feature extraction algorithm (EPRFE), a new elemental property based feature space was established. Band gap prediction RMSE has a small drop compared to 0.298 eV and the relative importance of elemental properties for band gap prediction was found. Finally, band gap and band offset of all nitrides in the design space were predicted and it was noticed that as the number of cation types increases, band gap tends to go up while band offset tends to go down. Since the predicted band-gaps distribute in all valuable band gap ranges, the predicted results will be useful for nitride design and discovery targeted towards various applications.
A Convex Approach to Path Tracking with Obstacle Avoidance for Pseudo-Omnidirectional Vehicles

This report addresses the related problems of trajectory generation and time-optimal path tracking with online obstacle avoidance. We consider the class of four-wheeled vehicles with independent steering and driving on each wheel, also referred to as pseudo-omnidirectional vehicles. Appropriate approximations of the dynamic model enable a convex reformulation of the path-tracking problem. Using the precomputed trajectories together with model predictive control that utilizes feedback from the estimated global pose, provides robustness to model uncertainty and disturbances. The considered approach also incorporates avoidance of a priori unknown moving obstacles by local online replanning. We verify the approach by successful execution on a pseudo-omnidirectional mobile robot, and compare it to an existing algorithm. The result is a significant decrease in the time for completing the desired path. In addition, the method allows a smooth velocity trajectory while avoiding intermittent stops in the path execution. (Less)
Observation of 
ψ(3686)→nn¯
 and improved measurement of 
ψ(3686)→pp¯

We observe the decay ψ(3686)→nn¯ for the first time and measure ψ(3686)→pp¯ with improved accuracy by using 1.07×108 ψ(3686) events collected with the BESIII detector. The measured branching fractions are B(ψ(3686)→nn¯)=(3.06±0.06±0.14)×10-4 and B(ψ(3686)→pp¯)=(3.05±0.02±0.12)×10-4. Here, the first uncertainties are statistical, and the second ones are systematic. With the hypothesis that the polar angular distributions of the neutron and proton in the center-of-mass system obey 1+αcos2θ, we determine the α parameters to be αnn¯=0.68±0.12±0.11 and αpp¯=1.03±0.06±0.03 for ψ(3686)→nn¯ and ψ(3686)→pp¯, respectively.
Recreational Demand in Bird Sactuary: The Case of Kapar Bird Sanctuary, Kelang, Malaysia

This study investigates the willingness to pay (WTP) for recreational resources at Kapar Bird Sanctuary (KBS), Kelang, Malaysia. The relevant values were estimated by utilizing dichotomous choice form of contingent valuation method (CVM). The logit models were used to analyze the data collected. Open-ended elicitation questions were used to induce respondents to state their maximum WTP, and the OLS model was employed to determine the WTP values. For the purpose of this study, a total 220 respondents were interviewed and asked their WTP for the conservation of KPS as an excitement place for recreational site. The findings of the study showed that the mean willingness to pay ranges from RM12.06 to RM60.94. This study implies that non-use value should be considered in policy making associated with recreational resources. The findings of this study are important in assists policy maker in management and development of recreational sites in Malaysia.
Apolipoprotein H, an Acute Phase Protein, a Performing Tool for Ultra-Sensitive Detection and Isolation of Microorganisms from Different Origins

Apolipoprotein H (ApoH), also known as beta2-glycoprotein I (s2-GPI), is a plasma glycoprotein of 50 kDa. ApoH is present in human plasma at a concentration of between 150 and 300 mg/ml (Bouma et al., 1999). In blood, ApoH circulate in free conformations or bound to lipoproteins: chylomicrons, very low-density lipoprotein (VLDL), low density lipoprotein (LDL) and high-density lipoprotein (HDL). In addition, ApoH has a high affinity for triglyceride-rich lipoproteins. The amount of ApoH associated with plasma lipoproteins in healthy individuals varies according to the authors from 4 to 13% (Gambino et al., 1999a) up to about 40% (Polz & Kostner, 1979). ApoH is able to activate lipoprotein lipases (Lee et al., 1983). ApoH was isolated from the fraction of plasma lipoproteins, and described for the first time in 1961 by H. Schultze E (Schultze, 1961). In a lesser extent, ApoH is also associated to s2-globulin fraction. ApoH is expressed in human liver, in intestinal cells and tissues (Averna et al., 1997). In rats, other sites of synthesis in low concentrations were identified as the kidney, small intestine, brain, cardiomyocytes of the heart, and at even lower in the spleen, stomach and prostate (Ragusa et al., 2006). ApoH is an acute phase protein and because when activated, ApoH bind, with a relative high affinity, to pathogens or their proteins, ApoH is also considered as an element of the host innate immune response, particularly during the acute phase. It is difficult to classified as positive or negative acute phase protein. This property is used as a mean to drastically improve diagnostic of pathogens from different origins, including human, animal or environmental and nature, including enveloped or non-enveloped viruses, parasites, and Gram+ or Gram – bacteria. Indeed, activated ApoH coupled to solid supports is used to concentrate and “clean” pathogens (from inhibitor of detection methods) to detect
Comparison of MODIS cloud microphysical properties with in-situ measurements over the Southeast Pacific

Utilizing the unique characteristics of the cloud over the Southeast Pacific (SEP) off the coast of Chile dur- ing the VOCALS field campaign, we compared satellite re- mote sensing of cloud microphysical properties against in- situ data from multi-aircraft observations, and studied the ex- tent to which these retrieved properties are sufficiently con- strained and consistent to reliably quantify the influence of aerosol loading on cloud droplet sizes. After constraining the spatial-temporal coincidence between satellite retrievals and in-situ measurements, we selected 17 non-drizzle compari- son pairs. For these cases the mean aircraft profiling times were within one hour of Terra overpasses at both projected and un-projected (actual) aircraft positions for two differ- ent averaging domains of 5 km and 25 km. Retrieved quan- tities that were averaged over a larger domain of 25 km com- pared better statistically with in-situ observations than aver- ages over a smaller domain of 5 km. Comparison at projected aircraft positions was slightly better than un-projected air- craft positions for some parameters. Overall, both MODIS- retrieved effective radius and LWP were larger but highly correlated with the in-situ measured effective radius and LWP, e.g., for averaging domains of 5 km, the biases are up to 1.75 µm and 0.02 mm whilst the correlation coefficients are about 0.87 and 0.85, respectively. The observed effec- tive radius difference between the two decreased with in- creasing cloud drop number concentration (CDNC), and in- creased with increasing cloud geometrical thickness. Com- pared to the absolute effective radius difference, the corre- lations between the relative effective radius difference and CDNC or cloud geometric thickness are weaker. For averag- ing domains of 5 km and 25 km, the correlation coefficients between MODIS-retrieved and in-situ measured CDNC are 0.91 and 0.93 with fitting slopes of 1.23 and 1.27, respec- tively. If the cloud adiabaticity is taken into account, better agreements are achieved for both averaging domains (the fit- ting slopes are 1.04 and 1.07, respectively). Our comparison and sensitivity analysis of simulated retrievals demonstrate that both cloud geometrical thickness and cloud adiabaticity are important factors in satellite retrievals of effective radius and cloud drop number concentration. The large variabili- ties in cloud geometrical thickness and adiabaticity, the de- pendencies of cloud microphysical properties on both quan- tities (as demonstrated in our sensitivity study of simulated retrievals), and the inability to accurately account for either of them in retrievals lead to some uncertainties and biases in satellite retrieved cloud effective radius, cloud liquid water path, and cloud drop number concentration. However, strong correlations between satellite retrievals and in-situ measure- ments suggest that satellite retrievals of cloud effective ra- dius, cloud liquid water path, and cloud drop number con- centration can be used to investigate aerosol indirect effects qualitatively.
DERIVATION OF MARKER GENE SIGNATURES FROM HUMAN SKIN AND THEIR USE IN THE INTERPRETATION TRANCRIPTIONAL CHANGES ASSOCIATED WITH DERMATOLOGICAL DISORDERS An expression atlas of human skin

Numerous studies have explored the altered transcriptional landscape associated with skin diseases to understand the nature of these disorders. However, data interpretation represents a significant challenge due to a lack of good maker sets for many of the specialised cell types that make up this tissue, whose composition may fundamentally alter during disease. Here we A cc ep te d A rti cl e This article is protected by copyright. All rights reserved. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/path.4864 have sought to derive expression signatures that define the various cell types and structures that make up human skin, and demonstrate how they can be used to aid the interpretation of transcriptomic data derived from this organ. Two large normal skin transcriptomics datasets were identified, one RNA-seq (n=578), the other microarray (n=165), quality controlled and subjected separately to network-based analyses to identify clusters of robustly co-expressed genes. The biological significance of these clusters was then assigned using a combination of bioinformatics analyses, literature and expert review. After cross comparison between analyses, 20 gene signatures were defined. These include expression signatures for hair follicles, glands (sebaceous, sweat, apocrine), keratinocytes, melanocytes, endothelia, muscle, adipocytes, immune cells, and a number of pathway systems. Collectively we have named this resource SkinSig. SkinSig was then used in the analysis of transcriptomic datasets for 18 skin conditions, providing in-context interpretation of these data. For instance, conventional analysis has shown there to be a decrease in keratinisation and fatty metabolism with age; we more accurately define these changes to be due to loss of hair follicles and sebaceous glands. SkinSig also highlighted the over-/under-representation of various cell types in skin diseases, reflecting an influx in immune cells in inflammatory disorders and a relative reduction in other cell types. Overall, our analyses demonstrate the value of this new resource in defining the functional profile of skin cell types and appendages, and in improving the interpretation of disease data.
Momentum Based Level Set Method For Accurate Object Tracking

This paper proposes a novel object tracking method that is robust to a cluttered background and large motion. First, a posterior probability measure (PPM) is adopted to locate the object region. Then the momentum based level set is used to evolve the object contour in order to improve the tracking precision. To achieve rough object localization, the initial target position is predicted and evaluated by the Kalman filter and the PPM, respectively. In the contour evolution stage, the active contour is evolved on the basis of an object feature image. This method can acquire more accurate target template as well as target center. The comparison between our method and the kernel- based method demonstrates that our method can effectively cope with the deformation of object contour and the influence of the complex background when similar colors exist nearby. Experimental results show that our method has higher tracking precision.
Dental Anatomic Variations in Primary Dentition: A Case Series

Many morphological variables have been identified both in primary and permanent dentitions. This report describes incidental finding of some uncommon dental traits like central accessory cusp or dens evaginatus, seventh accessory cusp in primary second molars and protostylid, triangular morphology of primary first molars. These characters have been amply documented in the permanent dentition. Presence of these extra cusps may have dental problems such as caries, sensitivity, occlusal interference and hence there is a need for continuous dental surveillance.
Sequence analysis of an ancient hemoglobin cDNA isolated from the moss Physcomitrella patens ( Accession No . AF 218049 )

Hemoglobins (Hbs) are ligand-binding hemoproteins that are found indiverse organisms. In plants, two classes of Hbs are known to exist:non-symbiotic (class I) and symbiotic (class II ) Hbs (Trevaskis etal., 1997; Arredondo-Peter et al., 1998; Hill, 1998) . The extensivelystudied symbiotic Hbs, such as leghemoglobins, are detected only innitrogen-fixing nodules where they facilitate the diffusion of oxygento bacteroids (Appleby, 1992). The recently discovered non-symbioticHbs are known to exist in both monocot and dicot plants, but theirfunction in plant organs is not known (Arredondo-Peter et al., 1998;Hill, 1998). The existence of non-symbiotic Hbs in monocots anddicots indicates that these proteins are widespread in floweringplants, and probably common to all land plants. Attempts to clone hbgenes from lower plants, such as liverworts and mosses, have beenunsuccessful probably because of the difficulty in preparing properprobes caused by the phylogenetic distance between lower and higherplants. Recently, an EST cDNA sequence (clone B46) isolated from themoss Physcomitrella patens was deposited in the GenBank database(Reski et al., 1998) and showed sequence similarity to soybeannon-symbiotic Hb.
The fraction of first- and second-generation stars in globular clusters - I. The case of NGC 6752

We present a new method to estimate the fraction of stars with chemical composition of first and second(s) generation(s) currently hosted in Galactic globular clusters (GCs). We compare cluster and field stars of similar metallicity in the [Fe/H]-[Na/H] plane. Since the phenomenon of multiple populations is only restricted to the cluster environment, the number of GC stars whose location coincides with that of field stars provides the fraction of first generation stars in that cluster. By exclusion, the fraction of second generation stars is derived. We assembled a dataset of 1891 field stars of the thin disk, thick disk, and halo of the Milky Way in the metallicity range -3.15 <= [Fe/H] <= +0.48 dex and with Na abundance from high resolution spectra. They are mostly dwarfs, but include also giants. Considering only the range in metallicity spanned by most GCs extensively studied for the Na-O anticorrelation (-2.36 <= [Fe/H] <= -0.33 dex), we have 804 stars. The total sample is homogeneized by offsets in [Fe/H] and [Na/H] with respect to a reference sample using the same line list and NLTE correction for Na adopted in a recent extensive survey of GC stars. This fully accounts for offsets among analyses due to different temperature scales, line lists, adopted (or neglected) corrections for departures from LTE. We illustrate our method estimating the fraction of first and second generation stars in the well studied GC NGC 6752. As a by-product, the comparison of [Na/H] values in GC and field stars suggests that at least two classes of old stellar systems probably contributed to the halo assembly: one group with characteristics similar to the currently existing GCs, and the other more similar to the present-day dwarf satellite galaxies.