3,387 research outputs found
Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum
No full textThis dataset includes genotype level trait values for 234 traits, some previously published and some unpublished, scored across the Sorghum Association Panel (SAP). It also includes all statistically significant GWAS hits identified when these same trait datasets were analyzed using either GLM, MLM, or FarmCPU GWAS algorithms as implemented in the MVP R package (https://github.com/xiaolei-lab/rMVP) with the genetic marker set first published in Miao et al 2020 (doi: https://doi.org/10.1104/pp.20.00277).
The second file titled "All_Significant_MashR_Peaks_lfsr0.001nadBayesFactor4.csv" contains all significant pleiotropic hits (Bayes Factor > 4 and lfsr
Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas-Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC (Preprint) "Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum" (doi: https://doi.org/10.1093/genetics/iyab087).
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Wavelength tunable 10-GHz 3-ps pulse source using a dispersion decreasing fiber-based nonlinear optical loop mirror
No full textWe experimentally demonstrate the use of a dispersion decreasing fiber (DDF)-based nonlinear optical loop mirror (NOLM) for the generation of wavelength tunable soliton-like pulses at a repetition rate of 10 GHz. We compress ~12 ps Gaussian pulses from an electro-absorption modulator (EAM) (followed by 125 m of DCF for preliminary linear dispersion compensation) into 3 ps pedestal-free pulses using both high-order soliton compression and nonlinear switching effects within an 8.5 km DDF-based loop mirror. The output pulses from the DDF-based NOLM show considerable pedestal reduction compared to those obtained by directly compressing the EAM seed pulses via a single passage through the DDF. Wavelength tuning of the compressed pulses over a ~15 nm bandwidth (from 1541 to 1556 nm) is demonstrated without a significant increase in pulse duration or degradation in pulse quality
Player agency in interactive narrative: audience, actor & author
No full textThe question motivating this review paper is, how can
computer-based interactive narrative be used as a constructivist learn-
ing activity? The paper proposes that player agency can be used to
link interactive narrative to learner agency in constructivist theory,
and to classify approaches to interactive narrative. The traditional
question driving research in interactive narrative is, ‘how can an in-
teractive narrative deal with a high degree of player agency, while
maintaining a coherent and well-formed narrative?’ This question
derives from an Aristotelian approach to interactive narrative that,
as the question shows, is inherently antagonistic to player agency.
Within this approach, player agency must be restricted and manip-
ulated to maintain the narrative. Two alternative approaches based
on Brecht’s Epic Theatre and Boal’s Theatre of the Oppressed are
reviewed. If a Boalian approach to interactive narrative is taken the
conflict between narrative and player agency dissolves. The question
that emerges from this approach is quite different from the traditional
question above, and presents a more useful approach to applying in-
teractive narrative as a constructivist learning activity
Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping
No full textThe definitive version is available at www.blackwell-synergy.co
Crop growth model-enabled genetic mapping of biomass accumulation dynamics in photoperiod-sensitive sorghum
No full textCrop growth rate is a critical physiological trait for forage and bioenergy crops like sorghum [Sorghum bicolor (L.) Moench], influencing overall crop productivity, particularly in photoperiod-sensitive (PS) types. Crop growth rate studies focus on either a physiological approach utilizing a few genotypes to analyze biomass accumulation or a genetic approach characterizing easily scorable proxy traits in larger populations. Thus, the genetic control of crop growth rate in terms of biomass accumulation is poorly understood in PS sorghum. In this study, we monitored biomass accumulation in a diverse panel comprising 269 PS sorghum accessions in two growing seasons. We performed sequential samplings at 11 timepoints, separating leaves from stems. For the total biomass and each fraction, we applied the beta growth function to determine the maximum crop growth rate (cm), maximum biomass accumulation (wmax), and time to cm (tm). Significant genetic variability was observed for all three parameters. Our analysis identified a practical window for cm assessment through accumulated biomass at 60–70 days after planting. Genome-wide association analysis suggested distinct and independent genetic controls of leaf and stem biomass accumulation, both physically and temporally. Common genomic regions were discovered controlling wmax and cm of stem and total biomass. These results provide new insights into the genetic control of crop growth rate, highlighting promising genomic regions for functional validation. This research also offers practical applications for plant breeding programs demonstrating the feasibility of selecting superior genotypes for both early and late biomass accumulation to enhance crop productivity.This article is published as Panelo, Juan S., Fernando E. Miguez, Patrick S. Schnable, and Maria G. Salas‐Fernandez. "Crop growth model‐enabled genetic mapping of biomass accumulation dynamics in photoperiod‐sensitive sorghum." The Plant Genome 18, no. 3 (2025): e70111. https://doi.org/10.1002/tpg2.70111USDA National Institute of Food and Agriculture, Grant/Award Numbers: Project #IOW05768, #IOW05730; Plant Sciences Institute, the Predictive Plant Phenomics Small Research Grant, and the R.F. Baker Center for Plant Breeding at Iowa State Universit
Charisma and Spirituality in the Early Church: A Study of Messalianism and Pseudo-Macarius
No full textThe thesis is an investigation into the concept of Charisma and Spirituality in the Early Church with particular emphasis upon the writings of Ps-Macarius, and of a group of ascetics known as the Messalians, evident in the late fourth / early fifth centuries. The Macarian writings are
examined to see what they reveal about the experiential pneumatic theology of the Early Church, the relationship between Syrian and Hellenic traditions of Christian Rhetoric, and the relationship between Ps-Macarius and the Cappadocian Circle. The Macarian corpus as a whole is examined to assess its rhetorical influences and style. The rhetoric of the Macarian corpus is seen to illustrate a high degree of sophistication. This study also gives definition to two terms that have become imprecise and diverse in their use: 'enkrateia' (self-control), and
`Syrian Christianity'. By isolating the characteristics of enkratefa the definitive stages of an encratic lifestyle are identified. The breaking down of the term into enkrateia, radical enkrateta and exclusive enkrateta enables a much clearer discussion to take place as to the
nature of the encratic theology of a group or individual. The final element of this study is a consideration of the distinct Macarian imagery that is evident within the corpus. Two images are considered in detail, the 'flight of the soul' and 'sober intoxication'. Overall this study
shows the variety of influences upon Ps-Macarius, and the uniqueness of his expression. The influences upon Ps-Macarius include a context of endemic Syrian spirituality, a radical encratic lifestyle, a Hellenic rhetorical training, and a distinct interpretation of Platonic and Neo-
Platonic images, coupled to the wider Judaic / Mesopotamian influences of his Church. It is shown that Ps-Macarius represents an individual voice that is distinct and recognisable amongst the Fathers of the Church
Nuclear translocation and signalling of L1-CAM in human carcinoma cells requires ADAM10 and presenilin/gamma-secretase activity
No full textL1-CAM (L1 cell-adhesion molecule), or more simply L1, plays an important role in the progression of human carcinoma. Overexpression promotes tumour-cell invasion and motility, growth in nude mice and tumour metastasis. It is feasible that L1-dependent signalling contributes to these effects. However, little is known about its mechanism in tumour cells. We reported previously that L1 is cleaved by ADAM (a disintegrin and metalloprotease) and that the cytoplasmic part is essential for L1 function. Here we analysed more closely the role of proteolytic cleavage in L1-mediated nuclear signalling. Using OVMz carcinoma cells and L1-transfected cells as a model, we found that ADAM10-mediated cleavage of L1 proceeds in lipid raft and non-raft domains. The cleavage product, L1-32, is further processed by PS (presenilin)/gamma-secretase to release L1-ICD, an L1 intracellular domain of 28 kDa. Overexpression of dominantnegative PS1 or use of a specific gamma-secretase inhibitor leads to an accumulation of L1-32. Fluorescence and biochemical analysis revealed a nuclear localization for L1-ICD. Moreover, inhibition of ADAM10 and/or gamma-secretase blocks nuclear translocation of L1-ICD and L1-dependent gene regulation. Overexpression of recombinant L1-ICD mediates gene regulation in a similar manner to full-length L1. Our results establish for the first time that regulated proteolytic processing by ADAM10 and PS/gamma-secretase is essential for the nuclear signalling of L1 in human carcinoma cell lines. Key words: a disintegrin and metalloprotease 10 (ADAM10), L1 cell-adhesion molecule (L1-CAM), nuclear translocation, presenilin (PS)/gamma-secretase activity, raft, signalling
Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance
No full textBackground: Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results: A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion: Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology. Keywords: next generation sequencing; short read assembly; Mollusc
LinoSPAD2: A 512×1 linear SPAD camera with system-level 135-ps SPTR and a reconfigurable computational engine for time-resolved single-photon imaging
No full textThe LinoSPAD2 camera combines a 512×1 linear single-photon avalanche diode (SPAD) array with an FPGA-based photon-counting and time-stamping platform, to create a reconfigurable sensing system capable of detecting single photons. The read-out is fully parallel, where each SPAD is connected to a different FPGA input. The hardware can be reconfigured to achieve different functionalities, such as photon counters, time-to-digital converter (TDC) arrays and histogramming units. Time stamping is performed by an array of 64 TDCs, with 20 ps resolution (LSB), serving 256 channels by means of 4:1 sharing. At sensor level, the pixel pitch is 26.2 μm with a fill factor of 25.1%. The median dark count rate of each SPAD at room temperature is below 100 cps at 6V excess bias, the single-photon timing resolution (SPTR) of each channel is 50 ps FWHM, and the peak photon detection probability reaches ~50% at 510 nm at the same excess bias. The fill factor can be increased by 2.3× by means of microlenses, with good spatial uniformity and flat spectral response above 400 nm. At system level, the average instrument response function (IRF) is 135 ps FWHM. The LinoSPAD2 camera enables a wide range of time-of-flight and time-resolved applications, including 3D imaging, fluorescence lifetime imaging microscopy (FLIM), heralded spectroscopy, and compressive Raman imaging, to name a few. Thanks to its features, LinoSPAD2 is a novel generation of reconfigurable single-photon image sensors capable of adapting their read-out and processing to match application-specific requirements, and combining SPAD arrays with advanced, massively-parallel computational functionalities. Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.QCD/DiCarlo La
Synthesis and Characterization of PEO-PS-PEO Triblock Copolymer Conjugated with Ni-NTA for Biosensors, 2018
No full textPoly(ethylene oxide)-poly(styrene)-poly(ethylene oxide) triblock copolymer with di-hydroxyl terminated groups (HO-PEO-PS-PEO-OH) was conjugated with nitrilotriacetic acid (NTA) via esterification reaction using N,N'-Dicyclohexylcarbodiimide (DCC), 4-Dimethylaminopyridine (DMAP) and Dimethylformamide (DMF) as a solvent at 80 ?C. The poly(ethylene oxide)-poly(styrene)-poly(ethylene oxide) with NTA end groups (NTA-PEO-PS-PEO-NTA) was characterized and structure confirmed by 1H NMR, 13C NMR, and FT-IR spectroscopies. Thermogravimetric analysis (TGA) was carried out to investigate the thermal stability of the starting triblock copolymer poly(ethylene oxide)-poly(styrene)-poly(ethylene oxide) with di-hydroxyl terminated groups (HO-PEO-PS-PEO-OH) and the conjugated poly(ethylene oxide)-poly(styrene)-poly(ethylene oxide) functional polymer (NTA-PEO-PS-PEO-NTA). Surface morphologies of the (HO-PEO-PS-PEO-OH) and (NTA-PEO-PS-PEO-NTA) were studied by atomic force microscopy. In addition, the size distributions were determined using dynamic light scattering. The thermal behavior of the (HO-PEO-PS-PEO-OH) and (NTA-PEO-PS-PEO-NTA) were examined by differential scanning calorimetry (DSC). DSC thermograms indicate the formation of a two phase polymer matrix. The poly(ethylene oxide)-poly(styrene)-poly(ethylene oxide) with NTA functionalized end groups (NTA-PEO-PS-PEO-NTA) was bound or chelated with Ni(II) metal ion. The binding studies were carried out by ultraviolet-visible (UV-Vis) spectroscopy. The electronic behaviors of PEO-b-PS-b-PEO/ PS/ NTA-PEO-b-PS-b-PEO-NTA with ratio (1/5/1) and PEO-b-PS-b-PEO/ PS/ NTA-PEO-b-PS-b-PEO-NTA-Ni containing 1% of oxidized single-walled carbon nanotubes (SWCNTs) were investigated by IV plots from Kelvin sensing. The IV plots before sensitizing with protein varied from the IV plots after binding with protein indicating that the composites may be used as active components in biosensors. KEYWORDS: Materials Chemistry, Polymer Chemistr
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