Quantitative imaging of the Dorsal nuclear gradient reveals limitations to threshold-dependent patterning in Drosophila

The NF-κB-related transcription factor, Dorsal, forms a nuclear concentration gradient in the early Drosophila embryo, patterning the dorsal-ventral (DV) axis to specify mesoderm, neurogenic ectoderm, and dorsal ectoderm cell fates. The concentration of nuclear Dorsal is thought to determine these patterning events; however, the levels of nuclear Dorsal have not been quantified previously. Furthermore, existing models of Dorsal-dependent germ layer specification and patterning consider steady-state levels of Dorsal relative to target gene expression patterns, yet both Dorsal gradient formation and gene expression are dynamic. We devised a quantitative imaging method to measure the Dorsal nuclear gradient while simultaneously examining Dorsal target gene expression along the DV axis. Unlike observations from other insects such as Tribolium, we find the Dorsal gradient maintains a constant bell-shaped distribution during embryogenesis. We also find that some classical Dorsal target genes are located outside the region of graded Dorsal nuclear localization, raising the question of whether these genes are direct Dorsal targets. Additionally, we show that Dorsal levels change in time during embryogenesis such that a steady state is not reached. These results suggest that the multiple gene expression outputs observed along the DV axis do not simply reflect a steady-state Dorsal nuclear gradient. Instead, we propose that the Dorsal gradient supplies positional information throughout nuclear cycles 10-14, providing additional evidence for the idea that compensatory combinatorial interactions between Dorsal and other factors effect differential gene expression along the DV axis

Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence

In early Drosophila embryos, the transcription factor Dorsal regulates patterns of gene expression and cell fate specification along the dorsal–ventral axis. How gene expression is produced within the broad lateral domain of the presumptive neurogenic ectoderm is not understood. To investigate transcriptional control during neurogenic ectoderm specification, we examined divergence and function of an embryonic cis-regulatory element controlling the gene short gastrulation (sog). While transcription factor binding sites are not completely conserved, we demonstrate that these sequences are bona fide regulatory elements, despite variable regulatory architecture. Mutation of conserved sequences revealed that putative transcription factor binding sites for Dorsal and Zelda, a ubiquitous maternal transcription factor, are required for proper sog expression. When Zelda and Dorsal sites are paired in a synthetic regulatory element, broad lateral expression results. However, synthetic regulatory elements that contain Dorsal and an additional activator also drive expression throughout the neurogenic ectoderm. Our results suggest that interaction between Dorsal and Zelda drives expression within the presumptive neurogenic ectoderm, but they also demonstrate that regulatory architecture directing expression in this domain is flexible. We propose a model for neurogenic ectoderm specification in which gene regulation occurs at the intersection of temporal and spatial transcription factor inputs

The effect of collagenase, water and calcium chloride on the removal of <i>Salmo salar</i> (salmon) and <i>Oncorhynchus mykiss</i> (trout) pin bones

The aim of this study was to determine the influence of the fillet structure on the deboning force required to remove salmon and trout pin bones. Salmon and trout fillets with differing fillet structure were used, in order to study the importance of the fillet structure on the deboning process. In the first test naturally gaping and non-gaping fillets were compared. To confirm the role that the collagen plays within the fillet structure, the fillets underwent series of treatments. Fillets were put into (i) a collagenase solution to remove the collagen in the fillet (ii) a calcium chloride solution to determine if collagen was the main influential factor. Both treated salmon and trout fillets were again compared to untreated fillets from the same batch. The results indicate that collagenase and calcium chloride have a large interaction on deboning force compared to water or no treatments

Deflation for inversion with multiple right-hand sides in QCD

Most calculations in lattice Quantum Chromodynamics (QCD) involve the solution of a series of linear systems of equations with exceedingly large matrices and a large number of right hand sides. Iterative methods for these problems can be sped up significantly if we deflate approximations of appropriate invariant spaces from the initial guesses. Recently we have developed eigCG, a modification of the Conjugate Gradient (CG) method, which while solving a linear system can reuse a window of the CG vectors to compute eigenvectors almost as accurately as the Lanczos method. The number of approximate eigenvectors can increase as more systems are solved. In this paper we review some of the characteristics of eigCG and show how it helps remove the critical slowdown in QCD calculations. Moreover, we study scaling with lattice volume and an extension of the technique to nonsymmetric problems

Variable typing: Assigning meaning to variables in mathematical text

Information about the meaning of mathematical variables in text is useful in NLP/IR tasks such as symbol disambiguation, topic modeling and mathematical information retrieval (MIR). We introduce variable typing, the task of assigning one mathematical type (multi-word technical terms referring to mathematical concepts) to each variable in a sentence of mathematical text. As part of this work, we also introduce a new annotated data set composed of 33,524 data points extracted from scientific documents published on arXiv. Our intrinsic evaluation demonstrates that our data set is sufficient to successfully train and evaluate current classifiers from three different model architectures. The best performing model is evaluated on an extrinsic task: MIR, by producing a typed formula index. Our results show that the best performing MIR models make use of our typed index, compared to a formula index only containing raw symbols, thereby demonstrating the usefulness of variable typing

Development and application of rice starch based edible coating to improve the postharvest storage potential and quality of plum fruit (<i>Prunus salicina</i>)

The study investigated the possibility of enhancing the shelf life of plum fruit coated with rice starch-ι-carrageenan (RS-ι-car) composite coating blended with sucrose fatty acid esters (FAEs). Film solution (starch 3%, carrageenan 1.5% and FAEs 2%) was prepared by mixing the ingredients and properties of stand-alone films (physical, mechanical, barrier and surface morphology) were studied before applying the coating on fruit surface. Fruit were stored at 20 °C for 3 weeks and analyzed for weight loss, ethylene production, respiration rate, color change, firmness, and titratable acidity (TA) and soluble solid content (SSC). Surface morphology of stand-alone film and fruit surface (after applying on the plum fruit) was studied using scanning electron microscopy (SEM). Phytochemical analysis was performed during the storage period and total phenolic content (TPC), total antioxidant capacity (TAC), flavonoid content (FC) and free radical scavenging activity were determined. The rice starch composite coating was shown to be effective in reducing both weight loss (WL) and respiration rate and inhibiting the endogenous ethylene production when compared to the uncoated control fruit stored at room temperature (p &lt; 0.05). TPC, TAC, FC and free radical scavenging activity was unaffected in the coated fruit throughout the storage period (p &lt; 0.05). The findings reported in this study indicate that the RS-ι-car-FAEs coating prolongs the shelf life and maintains the overall quality of plum fruit during storage and could potentially be commercialized as a new edible coating for the plum fruit industry

Strategic distortions in analyst forecasts in the presence of short-term institutional investors

We document that analysts cater to short - term investors by issuing optimistic target prices. Catering dominates among analysts at brokers without an investment banking arm as they face lower reputational cost. The market does not see through the analyst catering activity and their forecasts lead to temporary stock overpricing that short - term institutional investors exploit to offload their holdings to retail traders. We also report evidence consistent with catering brokers being rewarded with more future trades channelled through them. Our study identifies a new source of conflicts of interest in analyst research originating from the ownership composition of a stock

Application of neural networks to synchro-Compton blazar emission models

Jets from supermassive black holes in the centers of active galaxies are the most powerful persistent sources of electromagnetic radiation in the Universe. To infer the physical conditions in the otherwise out-of-reach regions of extragalactic jets we usually rely on fitting of their spectral energy distribution (SED). The calculation of radiative models for the jet non-thermal emission usually relies on numerical solvers of coupled partial differential equations. In this work machine learning is used to tackle the problem of high computational complexity in order to significantly reduce the SED model evaluation time, which is needed for SED fitting with Bayesian inference methods. We compute SEDs based on the synchrotron self-Compton model for blazar emission using the radiation code ATHE${\nu}$A, and use them to train Neural Networks exploring whether these can replace the original computational expensive code. We find that a Neural Network with Gated Recurrent Unit neurons can effectively replace the ATHE${\nu}$A leptonic code for this application, while it can be efficiently coupled with MCMC and nested sampling algorithms for fitting purposes. We demonstrate this through an application to simulated data sets and with an application to observational data. We offer this tool in the community through a public repository. We present a proof-of-concept application of neural networks to blazar science. This is the first step in a list of future applications involving hadronic processes and even larger parameter spaces.Comment: 12 pages, submitted, comments are welcome, code will be soon available at https://github.com/tzavellas/blazar_m

Variability of Pennsylvanian-Permian Carbonate Associations and Implications for NW Pangea Palaeogeography, East-Central British Columbia, Canada

Different stages of Pennsylvanian-Permian carbonate sedimentation in east-central British Columbia record a complex history of changing environments influenced by evolving palaeogeography and climate. Newly recognized tectonically controlled features affected the distribution and variability of carbonate associations, providing new interpretations for this portion of the west coast of Pangea. Both a heterozoan (cool water) and photozoan (warm-water) association were identified on either side of a palaeogeographic high here informally termed “Tipinahokan Peninsula”. Cool water carbonates were located outboard, or to the west of this high, an area influenced by upwelling waters. Inboard of this high, a warm, protected sea developed, here termed “Kisosowin Sea”. This configuration and palaeolatitude is similar to that of Baja California, Mexico and the Sea of Cortéz, providing a good modern analog for these deposits where warm water carbonates grow at latitudes otherwise dominated by cool water deposits. The warm sea provided a place for a photozoan association to develop during the Permian when the low latitude NW coast of Pangea was dominated by cool water carbonates