Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.
SIMULATION & MODELING OF BUSINESS PROCESSES

The main consequence of Business process reengineering as considered by many organizations is process view, statutory consistence (e.g. Securities and Futures Authority), response to marketplace services and the support of consolidated PC and data frameworks. This implies scrutinizing the manner by which organizations work and has suggestions for administration. Business process reengineering (BPR) and business-process simulation (BPS) maintain to ease process lucid. BPM conveys administration with a static organized strategy to business improvement, giving an "all encompassing" viewpoint on how the business works, and conveys a methods for reporting the business forms. Business processes are more and more accepted as the means to cutthroat endurance. Ongoing years have seen an expanding enthusiasm for techniques, strategies and apparatuses to help the upgrade of business processes under the standard of Business Process Modeling [BPM]. Inside the few strands of reasoning of BPM, the utilization of simulation has been growing quickly, as bore witness to by the expanding number of expert papers distributed in journals and conferences in the course of the most recent couple of years
Mise en évidence d'une fonction non-transcriptionnelle du facteur de transcription homéotique Cdx2

Le cancer colorectal (CCR) represente la 2eme cause de mortalite par cancer dans les pays industrialises. De nouveaux traitements permettant de bloquer l’evolution de la maladie sont necessaires. Il est donc important de mieux connaitre les acteurs impliques dans la cancerogenese. Lors du developpement du cancer, des genes suppresseurs de tumeur sont inhibes et des oncogenes sont actives, perturbant ainsi l’equilibre des cellules et les transformant. Au cours de ma these, je me suis interessee a deux genes homeotiques qui possedent des roles opposes dans les CCR. Cdx2 exerce un role suppresseur de tumeur, alors que HoxB7 agit comme un oncogene. Mon travail de these a permis (i) de mettre en evidence une nouvelle fonction non-transcriptionnelle de Cdx2 : inhibiteur de la reparation des cassures de l'ADN specifiquement dans le colon, (ii) et de reveler que le niveau d'expression des genes Cdx2 et Hoxb7 au sein de la tumeur peut avoir une importance pour le choix du traitement des CCR.
Analysis of communication pathways during seed development in Arabidopsis thaliana

Seed development in flowering plants requires coordination between the two genetically different fertilization products, the embryo and the endosperm and the surrounding maternal tissues, the integuments. However, little is known about the coordination of endosperm and embryo growth. In Arabidopsis, mutations in the cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) result in pollen that only successfully fertilizes the egg cell and seeds generated from crosses with cdka;1 pollen develop endosperm with solely maternal contribution. Here, fertilization by the cdka;1 mutant pollen was used to dissect early seed development. Crosses of 14 Arabidopsis accessions pollinated with cdka;1 mutant pollen revealed a large natural genetic variation with regard to the development of endosperm without paternal contribution. This work revealed a surprisingly large degree of autonomy in embryo growth, but also showed the embryo’s growth restrictions with regard to endosperm size. By using a recombinant inbred line population between the two Arabidopsis accessions Bayreuth-0 and Shahdara four QTLs were discovered, two main and four complex loci that influence the development of unfertilized endosperm. The genes of two DNA N-glycosylases ROS1 and DME, which catalyze the demethylation of symmetrical cytosine methylation, lay inside the two intervals of one of the two complex QTLs. A functional analysis revealed a new aspect of ROS1 and DME in restricting the proliferation of unfertilized endosperm. Moreover, ros1-dme double mutants could rescue the observed seed abortion upon cdka;1 pollination dependent on the activity of the methyltransferase MET1 during the sporophytic phase. Surprisingly, the rescue was independent of dme co-transmission, indicating an effect of ros1 together with dme in trans. The inheritance pattern of the mutant phenotypes revealed a paramutation-like phenomenon and the detection of almost 100% relative methylation levels on PHE1 and AGL36 sequence loci in ros1-dme double compared to the single mutants and Col-0 wild-type plants suggested that hypermethylation caused the mutant phenotype. The observed hypermethylation is likely to be established by in trans interactions between homologous DNA sequences on different chromosomes in a dominant paternal manner. These findings confirm previous results that endosperm formation is, beside other factors, triggered by the alteration of methylation levels prior to fertilization. Furthermore, DNA methylation patterns can probably be transferred via the paternal gametes, influencing not only the epigenetic status of the sporophyte, but also of the following gametophyte and affecting seed development after subsequent fertilization.
Design of a Wideband Variable-Gain Amplifier With Self-Compensated Transistor for Accurate dB-Linear Characteristic in 65 nm CMOS Technology

A simple yet effective approach for variable-gain amplifier (VGA) design with accurate dB-linear characteristic is presented. In order to extend the bandwidth of the designed VGA with a minimized footprint, an inductorless-based approach is adopted. Moreover, a unique approach that exploits a self-compensated transistor to compensate dB-linear gain error is proposed. Consequently, the overall VGA has an accurate dB-linear inherent characteristic without using any additional exponential generator for gain control. To prove the concept, the designed VGA is fabricated in a standard 65 nm CMOS technology. The measured results show that the voltage gain of the designed VGA can be controlled from −19 dB to 21 dB with a gain error less than 1 dB. Meanwhile, more than 4 GHz of bandwidth can be achieved for the entire gain range. The power consumption of the VGA, excluding the output buffer, is 3.9 mW. The core circuit of this design only occupies an area of 0.012 mm2.
Estudio comparativo del melanismo en lagartijas del grupo Liolaemus fitzingerii (Liolaemini: Liolaemus)

Color patterns and melanism have been focus of evolutionary studies in a wide variety of taxa, including lizards, and are often associated with certain ecological attributes. However, within the genus Liolaemus, only some particular aspects of melanism have been studied in a few species of the L. fitzingerii group. Populations of these species show different degrees of melanism with respect to both the intensity and location of black pigment, that in some cases have been used as diagnostic characters in different species of this group. The aim of this study was to assess the degree of polymorphism in ventral body and dorsal head melanism in Patagonian lizards from the five haploclades of the L. fitzingerii group (which includes all described species, except L. dumerili and L. camarones), to determine patterns of geographic variation and evaluate their usefulness as diagnostic characters. Our results show a high degree of polymorphism in both, ventral body and dorsal head melanism in the five haploclades, and in the different geographic regions analyzed. In this group, the melanic characters should be used with caution and in combination with others for diagnostic characters for species delimitation and diagnosis.
Drought-induced growth decline of Aleppo and maritime pine forests in south-eastern Spain.

Climate warming may enhance the negative effects of droughts on radial growth in areas with severe water deficit, such as Mediterranean mountains under semi-arid conditions. The impacts of drought on growth decline of Mediterranean pines have not been evaluated considering species with different vulnerability and areas with contrasting climates. Dendrochronological methods were used to assess the responses of basal area increment to drought in Pinus pinaster and P. halepensis plantations. We compared growth trends of trees with different defoliation degree in two sites in south-eastern Spain (Sierra de los Filabres and Sierra de Baza) with contrasting climatic conditions. In the more xeric area (Filabres) both pine species showed a sharp growth reduction in response to extreme droughts such as those observed in 1994-1995, 1999 and 2005. The radial growth of both species was enhanced by May and June precipitation of the year of tree-ring formation. P. pinaster showed higher defoliation in the xeric area (Filabres) than in the more mesic area (Baza) but needle loss was not linked to an abrupt growth reduction. Contrastingly, divergent radial growth patterns between trees showing high and low defoliation degrees were found for P. halepensis in the more xeric area, where a negative relationship between recent basal area increment and defoliation was found. Pine plantations in Mediterranean mountains under semi-arid conditions are highly vulnerable to warming-induced droughts. Such marginal stands constitute valuable monitoring systems to assess the negative impacts of drought on tree growth, and to test if management strategies as thinning can mitigate the negative impacts of climate warming on similar drought-stressed forests.
Quantifying relationships between land-use gradients and structural and functional indicators of stream ecological integrity

Summary 1. Modification of natural landscapes and land-use intensification are global phenomena that can result in a range of differing pressures on lotic ecosystems. We analysed national-scale databases to quantify the relationship between three land uses (indigenous vegetation, urbanisation and agriculture) and indicators of stream ecological integrity. Boosted regression tree modelling was used to test the response of 14 indicators belonging to four groups – water quality (at 578 sites), benthic invertebrates (at 2666 sites), fish (at 6858 sites) and ecosystem processes (at 156 sites). Our aims were to characterise the ecological response curves of selected functional and structural metrics in relation to three land uses, examine the environmental moderators of these relationships and quantify the relative utility of metrics as indicators of stream ecological integrity. 2. The strongest indicators of land-use effects were nitrate + nitrite, delta-15 nitrogen value (δ15N) of primary consumers and the Macroinvertebrate Community Index (a biotic index of organic pollution), while the weakest overall indicators were gross primary productivity, benthic invertebrate richness and fish richness. All indicators declined in response to removal of indigenous vegetation and urbanisation, while variable responses to agricultural intensity were observed for some indicators. 3. The response curves for several indicators suggested distinct thresholds in response to urbanisation and agriculture, specifically at 10% impervious cover and at 0.1 g m−3 nitrogen concentration, respectively. 4. Water quality and ecosystem process indicators were influenced by a combination of temperature, slope and flow variables, whereas for macroinvertebrate indicators, catchment rainfall, segment slope and temperature were significant environmental predictor variables. Downstream variables (e.g. distance to the coast) were significant in explaining residual variation in fish indicators, not surprisingly given the preponderance of diadromous fish species in New Zealand waterways. The inclusion of continuous environmental variables used to develop a stream typology improved model performance more than the inclusion of stream type alone. 5. Our results reaffirm the importance of accounting for underlying spatial variation in the environment when quantifying relationships between land use and the ecological integrity of streams. Of distinctive interest, however, were the contrasting and complementary responses of different indicators of stream integrity to land use, suggesting that multiple indicators are required to identify land-use impact thresholds, develop environmental standards and assign ecological scores for reporting purposes.
A Compact Mass-producible E-band Bandpass Filter Based on Multi-layer Waveguide Technology

This paper presents the design, implementation and experimental validation of a bandpass filter for high-data rate point-to-point link applications at E-band. The proposed design is developed in multilayer waveguide (MLW) technology, where an air-filled waveguide transmission line is formed by stacking several unconnected thin metal plates. Our MLW bandpass filter is designed by combining low-pass and high-pass filtering structures, and consists of 19 separate metal layers. An array of glide-symmetric holes, which act as an electromagnetic band gap (EBG) structure, are used to prevent any possible field leakage due to the air gaps between the layers. The fabricated filter provides a bandpass from 71.5 to 76 GHz with measured return loss better than 15 dB, and insertion loss better than 1.3 dB. The investigation of the potential for mass-production, as well as an evaluation of the MLW filter response for temperature variations from $- 30 ^{\circ }\mathrm {C}$ to $+ 70 ^{\circ }\mathrm {C}$ are discussed in this paper. The measured results show that the MLW filter has a center frequency thermal stability parameter of 9.3 ppm$/ ^{\circ }\mathrm {C}$, and center frequency drift of less than 0.12% over the whole temperature range. These results confirm the advantages of MLW technology for implementing ultra-compact bandpass filters showing low loss and potential for being mass-produced at millimeter-wave frequencies.
A comparative study on plant morphology, gas exchange parameters, and antioxidant response of Ocimum basilicum L. and Origanum vulgare L. grown on industrially polluted soil

The effects of Cd, Pb, and Zn uptake on plant morphology, photosynthetic parameters, antioxidant potential, and essential oil yield and quality in Ocimum basilicum L. and Origanum vulgare L. plants were evaluated. The plants were grown as a pot experiment in soil heavily polluted with Cd and Pb and on unpolluted soil. Both plants accumulated Cd, mainly in the roots, while Pb occurred in the oregano shoots only. The leaf blade thickness of both plants increased when grown in polluted soil. Basil plants responded to the action of heavy metals with increases in gas exchange , stomatal conductivity, and transpiration, but water-use efficiency declined. Gas exchange and transpiration were reduced in treated oregano plants, but stomatal conductivity and water-use efficiency increased significantly. In basil, the increased levels of low molecular weight antioxidants such as phenols and flavonoids were observed, while in oregano, ascorbate, glutathione, and phenols were enhanced. Enzymatic antioxidant defense was observed in both plants when grown in contaminated soil, mainly with glutathione peroxidase, quaiacol peroxidase, glutathione S-transferase, and glutathione reductase. Accumulated levels of Cd, Pb, and Zn in plant organs resulted in a reduction in essential oil yield in basil only.
iDEG: a single-subject method utilizing local estimates of dispersion to impute differential expression between two transcriptomes

Background Accurate profiling of gene expression in a single subject has the potential to be a powerful precision medicine tool, useful for unveiling individual disease mechanisms and responses. However, expression analysis tools for RNA-sequencing (RNA-Seq) data require replicate samples to estimate gene-wise data variability and make inferences, which is costly and not easily obtainable in clinical practice. Strategies to implement DEGSeq, DESeq, and edgeR for comparing two conditions without replicates (TCWR) have been proposed without evaluation, while NOISeq-sim was validated in a restricted way using qPCR on 400 transcripts. These methods impose restrictive assumptions in TCWR limiting inferential opportunities. Methods We propose a new method that borrows information across different genes from the same individual using a partitioned window to strategically bypass the requirement of replicates per condition. We termed this method “iDEG”, which identifies individualized Differentially Expressed Genes in a single subject sampled under two conditions without replicates, i.e., a baseline sample (unaffected tissue) vs. a case sample (tumor). iDEG transforms RNA-Seq data such that, under the null hypothesis, differences of transformed expression counts follow a distribution and variance calculated across a local partition of related transcripts at baseline expression. This transformation enables modeling genes with a two-group mixture model from which the probability of differential expression for each gene is then estimated by an empirical Bayes approach with a local false discovery rate control. To compare the performance of iDEG to other methods applied to TCWR, we conducted simulations assuming a Negative Binomial distribution with varying dispersion parameters and percentages of differentially expressed genes (DEGs). Results Our extensive simulation studies demonstrate that iDEG’s F1 accuracy scores better than the other methods at 5%90% and recall>75% and low false positive rate (<1%) in most conditions. Conclusion The partitioned window strategy provides a novel and accurate way to borrow information across genes locally and would probably increase the accuracy of all relevant methods.
Divergence and speciation in the Carpathians area: patterns of morphological and genetic diversity of the crane fly Pedicia occulta (Diptera:Pediciidae)

Abstract Morphological and genetic data are increasingly used in combination to test taxonomic hypotheses of species status. We compared the morphological and genetic diversity of the spring-dwelling crane fly, Pedicia occulta (Diptera), a widely distributed western Palearctic species considered to be monotypic throughout its range. We studied 11 morphological characters from 360 male individuals from the entire recorded range of P. occulta, and analyzed a subset of 77 individuals from the southeastern Carpathians, Rila, Pirin, and Rhodope for genetic variation at the mitochondrial cytochrome c oxidase I subunit (COI) gene. In contrast to expectations, our data on morphology and genetic structure of populations showed a structured pattern in the Carpathian region. Two well-separated groups were identified with nonmetric multidimensional scaling based on morphology. COI data revealed 2 divergent lineages (13.4% sequence distance) that corresponded to the 2 morphological groups and to differences in phenology and behavior. Sequence data showed additional genetic subdivision within one of these morphological groups, perhaps indicating the existence of additional cryptic entities. Our results also point out the importance of the Carpathian spring and mountain aquatic ecosystems as Pleistocene refugia. Our study emphasizes the power of combining morphological, genetic, and behavioral approaches in taxonomic hypothesis testing.
Lentiviral-mediated gene transfer – a patent review

Background: Lentiviral vectors are at the forefront of gene delivery systems for research and clinical applications. This special position is mainly due to their capacity to transduce slow dividing and non-dividing cells, to insert large genetic constructs in the host chromatin, and to sustain stable long-term transgene expression. Objective: To review the current literature and patents concerning the lentiviral system, the safety improvements, the production and purification of lentiviral vectors, pseudotyping and preclinical and clinical studies to provide expert opinion about the use of lentiviral vectors for gene therapy. Methods: The National Library of Medicine (PubMed) was searched for studies investigating the lentiviral system and the patents were searched at the World Intellectual Property Organization, European Patent Office and US Patent Office websites/databases. Results/conclusion: Based on the literature, several improvements have been performed regarding the safety, pseudotyping, vector production and purification on the lentivirus system. Clinical trials are underway for five different disorders.
Cladistic analysis and taxonomic revision of the genus Karos Goodnight & Goodnight, 1944 (Opiliones, Laniatores, Stygnopsidae)

A cladistic analysis of the genus Karos Goodnight & Goodnight, 1944, was performed using morphological data of the somatic and male genitalia characters. The analysis included 23 terminal taxa, including nine of the 11 described species of the genus plus nine new species according to the previous generic diagnosis and five species as outgroups. According to the topologies obtained by parsimony analyses, the genus is a paraphyletic assemblage, referred here as the Karos genus-group. Therefore, the genus Karos is rediagnosed here and now includes seven species: Karos barbarikos Goodnight & Goodnight, 1944 (type), Karos parvus Goodnight & Goodnight, 1971, Karos projectus Goodnight & Goodnight, 1971, Karos hexasetosus sp. nov., Karos monjarazi sp. nov., Karos singularis sp. nov., and Karos tersum sp. nov. The genera Monterella Goodnight & Goodnight, 1944, Montabunus Goodnight & Goodnight, 1945, Chapulobunus Goodnight & Goodnight, 1946, and Potosa Goodnight & Goodnight, 1947 are revalidated, rediagnosed, their respective type species are redescribed and the following species are described: Chapulobunus poblano sp. nov. and Potosa reddelli sp. nov. The genera Crettaros gen. nov., Huasteca gen. nov., and Mictlana gen. nov., and the following species are described: Crettaros santibanezi sp. nov. (type), Crettaros valdezi sp. nov., and Huasteca silhavyi sp. nov. The following new combinations are proposed: Huasteca gratiosa (Goodnight & Goodnight, 1971) comb. nov. (type), Huasteca rugosa (Goodnight & Goodnight, 1971) comb. nov. and Mictlana inops (Goodnight & Goodnight, 1971) comb. nov. (type). Karos brignolii Silhavý, 1974, is considered a junior synonym of Huasteca rugosa. Finally, ‘Karos’ depressus Goodnight & Goodnight, 1971 is considered incertae sedis until adult males can be studied. Diagnoses of the Karos and Paramitraceras genus-groups, and an identification key to the eight genera and 19 species of the former are provided. © 2015 The Linnean Society of London