Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Early embryogenesis-specific expression of the rice transposonPing enhances amplification of the MITE mPing

Miniature inverted-repeat transposable elements (MITEs) are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu), mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP), and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP). Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution. Citation: Teramoto S, Tsukiyama T, Okumoto Y, Tanisaka T (2014) Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing. PLoS Genet 10(6): e1004396. doi:10.1371/journal.pgen. 1004396 Editor: Cédric Feschotte, University of Utah School of Medicine, United States of America Received December 25, 2013; Accepted April 6, 2014; Published June 12, 2014 Copyright: 2014 Teramoto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan in the form of Grants-in-Aid for Scientific Research (21380004 and 25292006). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: takuji@kais.kyoto-u.ac. jp
Identification and Functional Characterization of G 6 PC 2 Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the G 6 PC 2-ABCB 11 Locus

Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants inG6PC2 (p.Val219Leu, p.His177Tyr, and p Tyr207Ser) influencing FG levels, conditionally independent of each other and the noncoding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishingG6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219LeuG6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights.
Evaluation of the “Quality of Education” in higher educational institutions (on the example of the Batumi State Maritime Academy)

The article addresses the problem of higher education - improving the quality of graduates' professional training, provides a brief analysis of research results, Recommendations on how to use the results “Quality of education” is a complex characteristic of education, the task of which is to train specialists who are competitive in the world market. It is impossible to develop a single, scientifically based system of indicators for the quality of student training, since the education system is different in all countries of the World, moreover, a different system of training students, which is one of the influencing factors on the quality of Higher Education. It is necessary to take into account the specifics of the university. One of the elements of the quality assessment system is monitoring, which is considered to be a comprehensive system for diagnosing the quantitative and qualitative characteristics of the effectiveness of an educational system. The assessment of the quality of education should be formed as a cumulative indicator of all the qualities that influence the educational process. During the work we used the results of sociological research of the subjects of the educational process: students, teachers, monitoring of the educational process (academic performance of students).
Microsatellites from sponge genomes: the number necessary for detecting genetic structure in Hemimycale columella populations

Using next-generation sequencing technology, we designed a pool of microsatellite primers and amplified them in 2 physically isolated populations of the Atlanto-Mediterranean sponge Hemimycale columella, which exhibits particular evolutionary, biological, and ecological features. The species has contrasting life cycles in shallow and relatively deep waters, and releases small, predictably low-dispersal larvae. This study experimentally evaluated how many polymorphic microsatellites would be necessary to detect genetic structure in H. columella popu- lations, and whether or not the use of compound loci is advisable. By sequencing 1/2 454 GS-FLX run, we obtained a total of 4208 sequences enclosing microsatellite motifs. We selected 20 micro- satellites, 15 of which proved adequate for the genetic study of the sponge populations. The 2 ana- lyzed populations were genetically structured with all microsatellite combinations assayed, and the values of the Dest and FST statistics did not increase with increasing number of loci. A weak sig- nal of genetic structure, however, was shown in bar plots representing membership coefficients for each individual to each sampling location even with all loci. We conclude that a few polymor- phic loci can detect structure in H. columella populations, but using 12 or more loci notably enhances the power of the analyses. The study also describes a low-cost protocol for obtaining microsatellites by the hundreds from non-model, ecologically relevant species, which can be used to provide information about population isolation, adaptation, and vulnerability.
Expectations from Administrative Reforms: An Attempt to Implement the Balanced Scorecard in a Public Sector Organization

The aim of this case study is to explore what actors in a Swedish municipality expect from a new administrative reform (i.e., an attempt to implement the Balanced Scorecard). The findings show that the expectations on changes are highest among the politicians, moderate among the administrators, and lowest among the operative employees. The differences can be explained by the way the reform is anticipated to favor or disfavor the actors, who in turn are influenced by the actors' past experiences. Most of the expressed expectations concern expectations of the outcome of the administrative reform, but some concern expectations on the reform itself.
Effect of bone morphogenetic protein-4 ( BMP4 ) on cardiomyocyte differentiation from mouse embryonic stem cell

The present study was designed to evaluate the effect of BMP-4 on mouse embryonic stem cells (ESCs)-derived cardiomyocyte. Cardiac differentiation of the mouse ESCs was initiated by embryoid bodies (EBs) formation in hanging drops, transfer of EBs to the suspension culture and then plating onto gelatin-coated tissue culture plates. BMP-4 was added to culture medium throughout the suspension period. Cultures were observed daily with an inverted microscope for the appearance of contracting clusters. At the early, intermediate and terminal stages of differentiation, the choronotropic responses of cardiomyocytes to cardioactive drugs were assessed, and the cardiomyocytes immunostained for cardiac troponin I, desmin, -actinin and nebulin. The contracting clusters were isolated for ultrastructural evaluation, at day 14 after plating. Moreover, total RNA extracted from contracting EBs of early and terminal stages of differentiation were examined for oct-4, and -myosin heavy chain, myosin light chain-2V and atrial natriuretic factor expression. The BMP-4 treatment resulted in a decrease in the percent of beating EBs and the percent of developing cardiomyocytes per EBs. As a whole, the chronotropic responses of beating cardiac clusters to cardioactive drugs in control group were better than BMP-4 treated group. The cardiomyocytes of both groups were positive immunostained for applied antibodies except for nebulin. Moreover, in the BMP-4 treated group, the ultrastructural characteristics and cardiac-specific genes expression were all retarded in the terminal stage of cardiomyocytes development. In conclusion, BMP-4 had an inhibitory effect on cardiomyocyte differentiation from the mouse ESCs in terms of ultrastructural characteristics, genes expression and functional properties. ' 2006 Elsevier Ireland Ltd. All rights reserved.
Reinforcement Learning Competition : Helicopter Hovering with Controllability and Kernel-Based Stochastic Factorization

The first approach is a smart exploration strategy developed by Gehring & Precup (2013), and the second one is a kernel-based algorithm recently presented by Barreto et al. (2011; 2012). We refer the reader to the original papers for a detailed description of the algorithms. Here we only provide overviews followed by a brief discussion of the algorithms’s performance on the helicopter task. We start by presenting some common background material and then we proceed to discuss each approach in particular.
Hyp x a i duces H 2 O 2 production and activ tes antioxidant defence system in grapevine buds through mediation of H 2 O 2 and ethylene

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short(6 h) and long(2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.
Global Extent of Early Eocene Hyperthermal Events: A New Pacific Benthic Foraminiferal Isotope Record From Shatsky Rise (ODP Site 1209)

Studying the dynamics of past global warming events during the late Paleocene to middle Eocene informs our understanding of Earth's carbon cycle behavior under elevated atmospheric pCO2 conditions. Due to sparse data coverage, the spatial character of numerous hyperthermal events during this period is still poorly constrained. Here we present a high‐resolution, benthic foraminiferal stable isotope record for northwest Pacific ODP Site 1209 (Leg 198) spanning 44 to 56 Ma with 5 kyr resolution. An existing Paleocene section was extended into the middle Eocene creating an unprecedented 22 Myr single‐site record. Several identified carbon isotope excursions correspond in timing and magnitude to hyperthermal layers previously described elsewhere. Maxima in scanning X‐ray fluorescence Fe intensities and pronounced minima in the wt% coarse fraction characterize carbonate dissolution for all of the hyperthermal events. The new astronomically calibrated stable oxygen isotope record assists in defining the onset, duration, and demise of the Early Eocene Climate Optimum (EECO, 49.14 to 53.26 Ma) and the onset of global cooling after the EECO (49.14 Ma). The cooling trend was interrupted by two warming episodes at 47.2 and 46.7 Ma. A major positive shift in the benthic foraminiferal carbon isotope record occurring from 51.2 to 51.0 Ma is now confirmed to be global. Benthic foraminiferal δ13C records from Atlantic and Pacific Oceans converge from 52.0 to 47.5 Ma pointing to a closer connection of deepwater convection initiating well in advance of the final connection ~40 Ma ago or an increase in bottom water formation around Antarctica.
Progress in high efficiency processing of EFG silicon solar cells

In contrast to standard block cast multicrystalline material the performance of EFG material is strongly related to an efficient hydrogenation step. In conformance to former publications the temperature profile during firing of a hydrogen-rich PECVD SiNx layer strongly affects the effectiveness of hydrogenation. With improved firing conditions 17.9% in efficiency could be reached on 2x2 cm2 EFG solar cells using a photolithography based solar cell process. Minor improvements are further reached by a better passivated emitter at the front side of the solar cells, raising the efficiency to 18.2 %. In contrast to commonly used texturing methods plasma texturing at IMEC (meanwhile also at Konstanz) is able to further increase efficiencies on EFG material. A new solar cell process is available to replace the full area Al BSF (with moderate surface passivation quality) with a SiO2/SiNx stack of good surface passivation quality using laser fired contacts. The process is applicable for multicrystalline material including a good hydrogenation together with a high temperature stable passivation for the rear side. First results are encouraging on untextured solar cells (diced out to 2x2 cm2) resulting in 19.4 % efficiency on floatzone and 18.5 % efficiency on standard block cast multicrystalline material. It is planned to apply this process on EFG material to further increase the maximum efficiency for this material in the future.
Title Cerebral asymmetry in children when reading Chinese characters Permalink

This study examined cerebral asymmetry, especially in the hierarchical visual system, when reading Chinese characters. Twelve righthanded Chinese children (mean age = 11.6 years) were scanned while performing semantic and phonological tasks. Strong leftward asymmetry was found in the left inferior frontal cortex (BA44/45/47), the parietal lobule (BA40), and the cingulate cortex (BA24/32). In the visual system, we found significant left-hemispheric dominance in the fusiform cortex (BA19/37), but no asymmetry was found in the primary visual cortex (BA17/18). The differential results for the primary visual cortex versus high-order visual cortex (i.e., the fusiform cortex) are discussed in terms of the contribution of the logographic nature of Chinese characters to the asymmetry pattern in the hierarchical visual system. D 2005 Elsevier B.V. All rights reserved. Theme: Neural basis of behavior Topic: Cognition
Abrupt shift of typhoon activity in the vicinity of Taiwan and its association with the western North Paci fi c-East Asian climate change

An abrupt shift in the number of the typhoon influence on Taiwan is found in 2000. On average, 3.3 typhoons per year are noted before 2000 (1970-1999), but this rate increases to 5.7 typhoons per year after 2000 (2000-2006). This abrupt change is consistent with a northward shift of the typhoon track over the western North Pacific-East Asian region and an increase of typhoon frequency over the Taiwan-East China Sea region. The northward shift of the typhoon track is associated with favorable environmental conditions over the western North Pacific, namely, the weakening of the western North Pacific subtropical high, the strengthening of the Asian summer monsoon trough, and an enhanced positive vorticity anomalies in the lower troposphere. Such conditions for shifting the typhoon track northward are induced by the warm SST anomalies over the equatorial western and central Pacific. JOURNAL OF CLIMATE 1
Free radical scavenging activity of some fungi indigenous to Tanzania

The objective of this study was to evaluate free radical scavenging capacity of crude extracts from forest basidiomycetous fungi, domestic zygomycetous fungi and marine ascomycetous fungi. Lethal concentration values that kill 50% of the brine shrimps (LC 50 ) were determined from 19 fungal extracts using brine shrimp test (BST). The LC 50 values of fungal extract ranged between 0.28–40µg/ml. The basidiomycetous ( Lactarius volemoides ) was the most toxic fungi with LC 50 of 0.28µg/ml while ascomycete Pichia guilliermondii showed the least toxicity with LC 50 of 40µg/ml. The concentrations of eleven fungal extracts were further evaluated on their ability to scavenge free radical using 1-diphenyl-2-picrylhydrazyl (α,α-diphenyl-β-picrylhydrazyl) (DPPH) as a dye reagent for spectrophotometric assay at 517nm. The extract concentrations that decreased the initial DPPH radical by 50% (EC 50 ) were determined. The EC 50 values ranged from 19–60. 4µg/ml ascorbic acid equivalents. Extracts from an edible but undomesticated basidiomycetous fungus isolated from Miombo forest and identified as Termitomyces microcarpus showed the highest scavenging effect with EC 50 at 19µg/ml while that from ascomycete Candida tropicalis showed the least EC 50 at 60. 4µg/ml. These results draw attention to wild undomesticated Miombo fungi as potential source of nutritional supplements worth further investigation.
OPTICS; ATOMS and MOLECULES; SPECTROSCOPY 1589 Progress in multipass tandem Fabry-Perot interferometry: I. A fully automated, easy to use, self-aligning spectrometer with increased stability and flexibility

A computer control for a Sandercock-type multipath tandem Fabry–Perot interferometer is described, which offers many advantages over conventionally used analog control: The range of stability is increased due to active control of the laser light intensity and the mirror dither amplitude. The alignment is fully automated enabling start of a measurement within a minute after start of align, including optionally finding the optimum focus on the sample. The software control enables a programmable series of measurements with control of, e.g., the position and rotation of the sample, the angle of light incidence, the sample temperature, or the strength and direction of an applied magnetic field. Built-in fitting routines allow for a precise determination of frequency positions of excitation peaks combined with increased frequency accuracy due to a correction of a residual nonlinearity of the mirror stage drive.
Kenaf as a Bioresource for Production of Hydrogen-rich Gas

The two-step gasification of biomass via carbonization-step followed by steam gasification, which produces hydrogen-rich water gas without any by products, was achieved using a small laboratory system. Carbonization of kenaf from 600 to 1000°C produced suitable chars for further steam gasification, which generated clean hydrogenrich gases without any byproducts. On the other hand, carbonization of kenaf at 400°C yielded an insufficient char that still contained raw chemical components, and generated hydrocarbons and tar-like materials during gasification. Importantly, the wood gas generated during carbonization had a sufficient Higher Heating Value (HHV) to serve as the heating source for the gasification. A lower gasification temperature induced the water-gas shift reaction, which led to a change the hydrogen content in the water gas composition. Raising the gasification temperature increased the specific HHV and decreased the gas yield. In addition, at these gasification temperatures, the H2 concentration in the water gases was greater than 58%, and the H2/CO ratio ranged from 1.8 to 3.0. On the other hand, increasing the steam supply rate decreased the specific HHV and CO yield and increased the H2 and CO2 yields. Therefore, the water-gas shift reaction played an important role under these conditions. On the basis of all of the above results, it was concluded that the water-gas reaction, C + H2O → CO + H2, leads to effective gasification of the kenaf char.
Impact of IVC housing on emotionality and fear learning in male C 3 H and B 6 J mice

Housing conditions are known to influence laboratory animal behaviour. However, it is not known whether housing mice in individually ventilated cages (IVCs) to maintain optimal hygienic conditions alters behavioural baselines established in conventional housing. This issue is important regarding comparability and reproducibility of data. Therefore, we investigated the impact of IVC housing on emotionality and fear learning in male C3HeB/FeJ (C3H) and C57BL/6J (B6J) mice housed singly either in conventional type II cages with wire bar lids (Conventional), or in IVCs of the same size, but with smooth, untextured lids (IVC classic), thus acoustically attenuated from external stimuli and with limited climbing facilities as compared to Conventional. To evaluate the role of climbing, additional mice were kept in IVCs with lids having wire bars (“grid”) added to the surface (IVC grid). Spontaneous behaviour, sensorimotor behaviour and fear learning were measured. IVC housing reduced activity and enhanced anxiety-related behaviour in both strains, whereas grooming latency was reduced in B6J only. IVC housing increased Acoustic Startle response in C3H, not in B6J mice. The “grid” did not compensate for these IVC housing effects. In contrast, B6J mice in IVC grid performed best in Fear Potentiated Startle, B6J mice in IVC classic performed worst, suggesting climbing facilities combined with IVC housing facilitate FPS performance in singly housed B6J males. Our data show that IVC housing can affect behavioural performance, and can modulate behavioural parameters in a general as well as a strainspecific manner, both relevant for mouse functional genomics.