Miracle-dz/UniFAR-FTUs huggingface dataset:
SNP discovery and applications in Brassica napus

This review summarises the biology, discovery and applications of single nucleotide polymorphisms in complex polyploid crop genomes, with a focus on the important oilseed crop Brassica napus. Brassica napus is an allotetraploid species, and along with soybean and oil palm is one of the top three most important oilseed crops globally. Current efforts are well underway to de novo assemble the B. napus genome, following the release of the related B. rapa 'A' genome last year. The next generation of genome sequencing, SNP discovery and analysis pipelines, and the associated challenges for this work in B. napus, will be addressed. The biological applications of SNP technology for both evolutionary and molecular geneticists as well as plant breeders and industry are far-reaching, and will be invaluable to our understanding and advancement of the Brassica crop species.
The Early Phase of /ɹ/ Production Development in Adult Japanese Learners of English

Although previous research indicates that Japanese speakers’ second language (L2) perception and production of English /ɹ/ may improve with increased L2 experience, relatively little is known about the fine phonetic details of their /ɹ/ productions, especially during the early phase of L2 speech learning. This cross-sectional study examined acoustic properties of word-initial /ɹ/ from 60 Japanese learners with a length of residence of between one month and one year in Canada. Their performance was compared to that of 15 native speakers of English and 15 low-proficiency Japanese learners of English. Formant frequencies (F2 and F3) and F1 transition durations were evaluated under three task conditions—word reading, sentence reading, and timed picture description. Learners with as little as two to three months of residence demonstrated target-like F2 frequencies. In addition, increased LOR was predictive of more target-like transition durations. Although the learners showed some improvement in F3 as a function of LOR, they did so mainly at a controlled level of speech production. The findings suggest that during the early phase of L2 segmental development, production accuracy is task-dependent and is influenced by the availability of L1 phonetic cues for redeployment in L2.
A Bethylid Wasp (Hymenoptera: Bethylidae) as a Promising Biocontrol Agent of Rosaceous Long Horn Beetle Ospheranteria coerulescens (Coleoptera: Cerambycidae)

ABSTRACT: Sclerodermus domesticus (Latreille, 1809) (Hym., Bethylidae) was collected from north eastern Iran, in association with larvae of Osphranteria coerulescens (Redtenbacher, 1850) (Coleoptera: Cerambycidae). The bethylids were found as larval ectoparasitoids on the longhorn beetle larvae. This parasitic wasp has gregarious activity with a high reproduction rate and parasitism potential. This is the first record of this parasitic wasp from Iran while O. coerulescens is recorded as a new host for this parasitoid. The parasitoid was identified using classic data accompanied with results of DNA sequences analysis of COI and 28S genes. In addition, we provide knowledge about biology of the parasitoid and present a discussion about its bionomics.
Ontogenic maturation of hemocyte production and gene expression in the hematopoietic system of Procambarus clarkii.

The red swamp crayfish, Procambarus clarkii is an important aquaculture decapod species as well as invasive species in some countries. The present study investigates the association between the moult stages-related pattern and the abundance of different cell types with the lymphoid organs of P. clarkii. Studies on the effect of moult cycle on the lymphoid organ spheroid (LOS) cells of P. clarkii were also studied. The spheroid to total tissue (STT) ratio of the lymphoid organ varied during the life span of the crayfish. Kazal-type serine proteinase inhibitor hcPcSP12 with complete cDNA sequence, were identified from cDNA library of the red swamp crayfish, P. clarkii. RT-PCR shows that hcPcSP12 exists mainly in hemocytes. Western both demonstrates that hcPcSP12 only exists in semi-granular cells. (Abdel-Hakim S. El-Din, Kohar G. Varjabedian, Rewaida A. Abdel-Gaber and Mai M. Mohamed. Ontogenic Maturation of Hemocyte Production and Gene Expression in the Hematopoietic System of Procambarus clarkii. J Am Sci 2013;9(2):213-220). (ISSN: 1545-1003). http://www.jofamericanscience. org . 30
Recycled stellar ejecta as fuel for star formation and implications for the origin of the galaxy mass–metallicity relation

We use cosmological, hydrodynamical simulations from the Evolution and Assembly of GaLaxies and their Environments and OverWhelmingly Large Simulations projects to assess the significance of recycled stellar ejecta as fuel for star formation. The fractional contributions of stellar mass-loss to the cosmic star formation rate (SFR) and stellar mass densities increase with time, reaching 35 and 19 per cent, respectively, at z = 0. The importance of recycling increases steeply with galaxy stellar mass forM* < 1010. 5M_, and decreases mildly at higher mass. This trend arises from the mass dependence of feedback associated with star formation and AGN, which preferentially suppresses star formation fuelled by recycling. Recycling is more important for satellites than centrals and its contribution decreases with galactocentric radius. The relative contribution of asymptotic giant branch (AGB) stars increases with time and towards galaxy centres. This is a consequence of the more gradual release of AGB ejecta compared to that of massive stars, and the preferential removal of the latter by star formation driven outflows and by lock up in stellar remnants. Recycling-fuelled star formation exhibits a tight, positive correlation with galaxy metallicity, with a secondary dependence on the relative abundance of alpha elements (which are predominantly synthesized in massive stars), that is insensitive to the subgrid models for feedback. Hence, our conclusions are directly relevant for the origin of the mass–metallicity relation and metallicity gradients. Applying the relation between recycling and metallicity to the observed mass–metallicity relation yields our best estimate of the mass-dependent contribution of recycling. For centrals with a mass similar to that of the Milky Way, we infer the contributions of recycled stellar ejecta to the SFR and stellar mass to be 35 and 20 per cent, respectively.
Planes Pre-Análisis para la investigación cualitativa

The design and registration of Pre-analysis Plans (PAP) represents a significant improvement in social science research transparency. This tool is commonly used in experimental research. In this research note, we suggest extending the use of PAP to qualitative research. In recent decades, researchers have produced several methodological innovations, which have improved the quality of qualitative analysis. New tools also have been developed and researchers have taken important steps to improve data collection and transparency in the analysis of qualitative data. The development of Pre-analysis Plan-Qualitative (PAP-Q) aims to synthetize these advances into a guide for researchers, in order to improve transparency and better specify the role of induction in the construction of causal arguments.
Development of transcriptome based web genomic resource of small cardamom

Small cardamom, scientifically known as Elettaria cardamomum belong to Zingiberaceae family and mostly cultivated in the tropical region of world. It is also called as “queen of spices” as it is most economical important spices crop which is famous due to its aroma and used in various medicinal purposes. Mosaic or katte diseases, the most destructive disease caused by Cardamom mosaic virus (CdMV), is the major biotic stress leading to the declination of crop production and greater economic loss. The paired end reads of control and mosaic virus infected samples of small cardamom was generated using illumina Hiseq 2000 technology for the identification of differential expressed genes which were associated with plant defense and plant immunity against mosaic disease. De novo transcriptome assembly was performed using trinity assembler followed by expression analysis and markers identification such as SSR, SNP and Indels. A total of 123338 transcripts were generated with N50 of 1520 bp, 5317 differential expressed genes, 24475 putative SSR markers, 147442 SNPs and 154217 Indels from control and mosaic virus infected samples respectively, 2267 transcriptional factors, 1219 domains and 807 families. We found some genes which may play an important role in plant defense and plant immunity such as disease resistance RGA1 and RGA3, RNA dependent RNA polymerase gene, LRR receptor-like serine threoninekinase, Mitogenactivated protein kinase kinase kinase (MAPKKK) ANP1-like, HSP81-1, NAC, PR1, Thaumatin-Like Protein (PR5), NBS-LRR, MYB, bHLH, WRKY. Further, 12 genes were selected from differential expressed analysis of RNA-seq for q-PCR validation experiment. In this study, we identified differential expressed genes as well as novel transcripts may play an important role in plant defense against mosaic disease, whereas mined markers and variants will be useful for breeder for development of disease resistant small cardamom crops. Also, we developed web transcriptomic resources “SmTMVD: Transcriptome Based Mosaic Virus Database in small cardamom (http://webtom.cabgrid.res.in/smtmvd/)” of small cardamom which can be useful for researchers all over the globe who are working on small cardamom.
Registration of ‘Renovation’ White Clover

‘Renovation’ (Reg. No. CV-9, PI 680615), is a large-leaved, synthetic intermediate type white clover (Trifolium repens f. hollandicum Erith ex Jav. & Soo) cultivar derived after hybridizing (i.e., population crosses) random, individual plants from a naturalized ecotype population from Oklahoma with those from the ‘Regal’, ‘Patriot’, ‘Tillman’, and ‘SRVR’ cultivars. Renovation was jointly developed, tested, and released in 2016 under the experimental designation NFWC04-49 by the Samuel Roberts Noble Foundation, Ardmore, OK, and the University of Georgia Research Foundation, Athens, GA. ‘Durana’, an intermediate type white clover cultivar, and Patriot, a ladino × intermediate population hybrid, demonstrated that persistent cultivars are possible based on intermediate germplasm. Renovation was found to be an intermediate type based on seedhead number comparable to Durana but higher than Regal (ladino type). Renovation’s leaf size is larger than Durana and equal to Patriot; its plant height and stolon characteristics are intermediate between Regal and Durana and more like Patriot. Renovation demonstrated animal performance and pasture growth rate much better than nitrogen-fertilized controls when overseeded into deteriorating tall fescue pastures in replicated paddocks grazed by beef steers. Renovation is licensed for commercial production and sales to Smith Seed Services, Halsey, OR.
Sphecid wasp larvae feeding on large-sized cockroaches in a dead wood cavity

We investigated the nest site and prey items of Isodontia auripygata (Hymenoptera: Sphecidae) in a subtropical forest on Iriomote Island, ca. 200 km east of Taiwan. I. auripygata used the cavity of a dead branch as their nest site, and the nest was composed of two cells that were divided by wood offcuts. Inside the branch, we found large-sized adult cockroaches, Rhabdoblatta formosana (Blattodea: Epilampridae), R. formosana adults were fed to an I. auripygata larva in each cell. To our knowledge, this is the third record of species of the genus Isodontia that prey on cockroaches.
Development of nanotechnology-based drug delivery systems with olive vegetable oil for cutaneous application

Liquid-Crystalline Systems represent active compounds delivery systems that may be able to overcome the physical barrier of the skin, especially represented by the stratum corneum. To obtain these systems, aqueous and oily components are used with surfactants. Of the different association structures in such systems, the liquid-crystalline offer numerous advantages to a topical product. This manuscript presents the development of liquid-crystalline systems consisting, in which the oil component is olive oil, its rheological characterizations, and the location of liquid crystals in its phase map. Cytotoxic effects were evaluated using J-774 mouse macrophages as the cellular model. A phase diagram to mix three components with different proportions was constructed. Two liquid crystalline areas were found with olive oil in different regions in the ternary diagram with two nonionic surfactants, called SLC1 (S1) and SLC2 (S2). These systems showed lamellar liquid crystals that remained stable during the entire analysis time. The systems were also characterized rheologically with pseudoplastic behavior without thixotropy. The texture and bioadhesion assays showed that formulations were similar statistically (p < 0.05), indicating that the increased amount of water in S2 did not interfere with the bioadhesive properties of the systems. In vitro cytotoxic assays showed that formulations did not present cytotoxicity. Olive oil-based systems may be a promising platform for skin delivery of drugs.
Two Arabidopsis late pollen transcripts are detected in cytoplasmic granules

Abstract Many of mRNAs synthesized during pollen development are translated after germination, and we hypothesize that they are stored in cytoplasmic granules. We analyzed the cellular localization of the SKS14 and AT59 Arabidopsis mRNAs, which are orthologues of the tobacco NTP303 and tomato LAT59 pollen mRNAs, respectively, by artificially labeling the transcripts with a MS2‐GFP chimera. A MATLAB‐automated image analysis helped to identify the presence of cytoplasmic SKS14 and AT59 mRNA granules in mature pollen grains. These mRNA granules partially colocalized with VCS and DCP1, two processing body (PB) proteins. Finally, we found a temporal correlation between SKS14 protein accumulation and the disappearance of SKS14 mRNA granules during pollen germination. These results contribute to unveil a mechanism for translational regulation in Arabidopsis thaliana pollen.
EVALUATION OF ANALYTICAL METHODS OF MICROBIAL ACTIVITY DURING SUCROSE EXTRACTION FROM SUGAR BEET

S u m m a r y The aim of our research was to verify selected methods to determine microbial activity during extraction process in term of speed, simplicity and accurancy of the analysis. Indirect methods ‐ enzymatic determination of L-lactic acid, isotachophoretic determination of lactic acid, pH, as well nitrite amounts determination were verified. The results of these methods were compared with those of direct one ‐ determination of bacteria counts (mesophilic and thermophilic bacteria). The determination of L-lactic acid by enzymatic device MICROZYM ‐ L is very simple and rapid. But in same cases L-lactic acid does not indicate a true microbial situation in extractor. The determination of total lactic acid (L + D isomers) is more adequate for detection of contamination in extractor. The results of the nitrite amount determination did not confirm the sanitary situation found out by measurment of lactic acid, pH and bacteria counts in some cases.
A simple and general method for accounting for phylogenetic uncertainty via Rubin’s rules in comparative analysis

Shinichi Nakagawa and Pierre de Villemereuil Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9054, New Zealand Laboratoire d’Ecologie Alpine (LECA-UMR CNRS 5553), Universite Joseph Fourier, BP 53, 38041 Grenoble, France Both authors contributed equally Running head: Phylogenetic uncertainty and Rubin’s rules *Correspondence: S. Nakagawa e-mail: s.nakagawa@unsw.edu. au !
Beyond metaphor in product use and interaction

The overall aim of this paper is to demonstrate that there is a need for supplementing the theory of product metaphor with a more elaborate theory of product meaning. More speci! cally, we argue that the notion of product metaphor neglects three critically important aspects of meaning making in product use. First, the notion of product metaphor usually accounts for how the visual form and appearance of a product might cue people to conceive of the product in terms of another conceptual source (e.g. a coffee maker as a butler), while leaving the role of cross-modal sensory experience in product meaning out of consideration. Secondly, like other theoretical frameworks in design semantics, the notion of product metaphor primarily accounts for the semantic operations that are involved in the ! rst initial phase of product categorization and interpretation, while eschewing the question as to how product interpretation might evolve over time as people interact with and use the product. Finally, in product use there often emerge more complex and even ambiguous forms of meaning, which fall outside the explanatory scope of the source-target construal principle – the key semantic principle of product metaphor. In order to remedy these limitations inherent in the theory of product metaphor we introduce a new semantic framework based upon Fauconnier and Turner’s theory of conceptual blends.
Transdisciplinary innovation research in Uzbekistan – one year of ‘Follow-the-Innovation’

In 2008, a German-funded interdisciplinary research project in Khorezm province, Uzbekistan, initiated a participatory approach to innovation development and diffusion with local stakeholders. Selected agricultural innovations, developed by the project and identified as ‘plausible promises’, have since then been tested and modified accordingly by teams of researchers, local farmers and water users. This paper discusses the challenges faced in this process of joint experimentation and learning between researchers and local stakeholders whose behaviours, attitudes and actions are heavily shaped by the local context, academic discipline and hierarchical culture of knowledge governance.
Cardiotoxicity of Plants in Iran: a Review

In this review an attempt has been made to review the cardiotoxic effects of poisonous plants which are found in Iran. Among various plant species growing in different regions of Iran, a large number of plants contain chemical compounds which are toxic to animals and humans. Among those poisonous plants, cardiotoxic plants are important due to the acute nature of their toxicity and frequent lethal livestock and human intoxications. Cardiotoxic plants of Apocynaceae family, Nerium oleander, N. indicum and Thevetia peruviana contain cardiac glycosides including oleandrin, oleandroside and thevetin A-C. Plants of Taxaceae family, Taxus baccata and T. brevifolia contain taxine alkaloids, including taxine A and B. The toxic effects of cardiac glycosides are primarily attributed to inhibition of plasmalemmal Na+/ K+-ATPase which results into the accumulation of intracellular Ca2+ and, depending to its severity, inotropic or arrhythmic effects are seen. Taxine B, the prominent alkaloid in Taxus spp. block sodium and calcium channels preferentially in cardiac myocytes, thus causing conduction abnormalities. Various cardiac arrhythmias in acute cases of poisoning with aforementioned plants result in acute heart failure and death. Post mortem findings are non-diagnostic and toxicological analysis of gastrointestinal tract content or body fluids is used for detection of cardiac glycosides and taxines.
Transformation of Conventional Houses to Smart Homes by Adopting Demand Response Program in Smart Grid

In an ever-growing state of electricity demand due to population growth as well as modernization of societies, it has compelled us to look for many options to cope with the situations. However, for a balanced electrical power demand and supply, it is necessary to respond requirement at any time without any interruption with the strategy of demand response programs (DRP) to the users. In order to promote smart usage of electrical power, smart grid networks are gradually transforming conventional grids in many places. As a part of smart grid, conventional houses may be transformed to smart house by simply implementing some intelligent controller with interfaces like smart plugs to the conventional electrical appliances. This chapter elaborates a new strategy of home energy management system (HEMS) in a smart grid environment to transform any ordinary premises to smart house to be energy efficient by simply rescheduling operation time.
Forest floor CO 2 flux measurements with a dark-light chamber

An automatic closed chamber system for measuring net carbon flux from the forest floor was equipped with both a transparent and an opaque cover. The system was operated in such way that a measurement session with transparent chamber was followed by a session with dark chamber. This made it possible to estimate besides total daytime respiration and nighttime respiration also the gross assimilation of the vegetation enclosed in the chamber. The chamber was used at two locations, Hyytiala in Finland and Norunda in Sweden. Results were compared to estimation of gross assimilation by extrapolation of nighttime respiration and the difference between daytime and nighttime respiration was analyzed. Estimated gross photosynthesis from the darkening sessions by the chamber resulted in a higher gross photosynthesis then obtained by extrapolation from nighttime respiration for Norunda, but not for Hyytala. Comparison of obtained gross photosynthesis rates indicated that the forest floor vegetation contributed up to 30% of maximum net ecosystem uptake.
Role of bias conditions in the hot carrier degradation of AlGaN/GaN high electron mobility transistors

The impacts of gate bias and device temperature on carrier energy distributions are reported for AlGaN/GaN High Electron Mobility Transistors. The lateral electric field and the average carrier energy are the highest at the end of gate on the gate-drain access side. The number of high energy carriers is the greatest in the semi-ON operating condition, with maximum energies exceeding the activation energy of defects in the AlGaN. There is a significant decrease in the number of very high energy carriers (greater than 2 eV) as the device temperature increases whereas the number of moderately energetic carriers (between 1 to 2 eV) is higher at elevated temperatures. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)