bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental Trajectories of Feeding Problems in Children with Autism Spectrum Disorder
Authors: Peverill Sarah , Smith Isabel M , Duku Eric , Szatmari Peter , Mirenda Pat , Vaillancourt Tracy , Volden Joanne , Zwaigenbaum Lonnie , Bennett Teresa , Elsabbagh Mayada , Georgiades Stelios , Ungar Wendy J 
Published: April 2019

AbstractObjectiveAlthough feeding problems are a common concern in children with autism spectrum disorder (ASD), few longitudinal studies have examined their persistence over time. The purpose of this study was to examine the developmental progression of feeding problems across four time points in preschoolers with ASD.MethodsGroup-based trajectory analyses revealed four distinct trajectories of feeding problems in our sample (N = 396).ResultsThe majority of children showed levels of feeding problems that were low from the outset and stable (Group 1; 26.3%) or moderate and declining over time (Group 2; 38.9%). A third group (26.5%) showed high levels of feeding problems as preschoolers that declined to the average range by school age. Few participants (8.3%) showed evidence of severe chronic feeding problems. Feeding problems were more highly correlated with general behavior problems than with autism symptom severity.ConclusionsOverall, our findings demonstrated that in our sample of children with ASD, most feeding problems remitted over time, but a small subgroup showed chronic feeding problems into school age. It is important to consider and assess feeding problems in ASD against the backdrop of typical development, as many children with ASD may show improvement with age.
The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon
Authors: Oren Elad , Tzuri Galil , Vexler Lea , Dafna Asaf , Meir Ayala , Faigenboim Adi , Kenigswald Merav , Portnoy Vitaly , Schaffer Arthur A , Levi Amnon , Buckler Edward S , Katzir Nurit , Burger Joseph , Tadmor Yaakov , Gur Amit 
Published: April 2019

AbstractColor and pigment contents are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigment content in the rind and flesh of mature melon fruits. A genome-wide association study (GWAS) of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation in this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent single nucleotide polymorphisms in the CmAPRR2 gene are causative of the light rind phenotype. The multi-haplotypic nature of this gene explains the lack of detection power obtained through genotyping by sequencing-based GWAS and confirms the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoid bio-fortification of cucurbit crops.
Nitric oxide accelerates germination via the regulation of respiration in chickpea
Authors: Pandey Sonika , Kumari Aprajita , Shree Manu , Kumar Vinod , Singh Pooja , Bharadwaj Chellapilla , Loake Gary J , Parida Swarup K , Masakapalli Shyam Kumar , Gupta Kapuganti Jagadis 
Published: April 2019

AbstractSeed germination is crucial for the plant life cycle. We investigated the role of nitric oxide (NO) in two chickpea varieties that differ in germination capacity: Kabuli, which has a low rate of germination and germinates slowly, and Desi, which shows improved germination properties. Desi produced more NO than Kabuli and had lower respiratory rates. As a result of the high respiration rates, Kabuli had higher levels of reactive oxygen species (ROS). Treatment with the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) reduced respiration in Kabuli and decreased ROS levels, resulting in accelerated germination rates. These findings suggest that NO plays a key role in the germination of Kabuli. SNAP increased the levels of transcripts encoding enzymes involved in carbohydrate metabolism and the cell cycle. Moreover, the levels of amino acids and organic acids were increased in Kabuli as a result of SNAP treatment. 1H-nuclear magnetic resonance analysis revealed that Kabuli has a higher capacity for glucose oxidation than Desi. An observed SNAP-induced increase in 13C incorporation into soluble alanine may result from enhanced oxidation of exogenous [13C]glucose via glycolysis and the pentose phosphate pathway. A homozygous hybrid that originated from a recombinant inbred line population of a cross between Desi and Kabuli germinated faster and had increased NO levels and a reduced accumulation of ROS compared with Kabuli. Taken together, these findings demonstrate the importance of NO in chickpea germination via the control of respiration and ROS accumulation.
Structural and functional imaging of large and opaque plant specimens
Authors: Hesse Linnea , Bunk Katharina , Leupold Jochen , Speck Thomas , Masselter Tom 
Published: April 2019

AbstractThree- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form–structure–function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.
A missense mutation in Large Grain Size 1 increases grain size and enhances cold tolerance in rice
Authors: Chen Xiaolong , Jiang Liangrong , Zheng Jingsheng , Chen Fangyu , Wang Tiansheng , Wang Meiling , Tao Yi , Wang Houcong , Hong Zonglie , Huang Yumin , Huang Rongyu 
Published: April 2019

Abstract
Grain shape is controlled by quantitative trait loci (QTLs) in rice (Oryza sativa L.). A rice mutant (JF178) with long and large grains has been used in a breeding program for over a decade, but its genetic basis has been unclear. Here, a semi-dominant QTL, designated Large Grain Size 1 (LGS1), was cloned and the potential molecular mechanism of LGS1 function was studied. Near-isogenic lines (NILs) and a map-based approach were employed to clone the LGS1 locus. LGS1 encodes the OsGRF4 transcription factor and contains a 2 bp missense mutation in the coding region that coincides with the putative pairing site of miRNA396. The LGS1 transcript levels in the mutant line were found to be higher than the lgs1 transcript levels in the control plants, suggesting that the mutation might disrupt the pairing of the LGS1 mRNA with miR396. In addition to producing larger grains, LGS1 also enhanced cold tolerance at the seedling stage and increased the survival rate of seedlings after cold stress treatment. These findings indicate that the mutation in LGS1 appears to disturb the GRF4–miR396 stress response network and results in the development of enlarged grains and enhancement of cold tolerance in rice.
StMYB44 negatively regulates anthocyanin biosynthesis at high temperatures in tuber flesh of potato
Authors: Liu Yuhui , Lin-Wang Kui , Espley Richard V , Wang Li , Li Yuanming , Liu Zhen , Zhou Ping , Zeng Lihui , Zhang Xiaojing , Zhang Junlian , Allan Andrew C 
Published: April 2019

Abstract
High temperatures are known to reduce anthocyanin accumulation in a number of diverse plant species. In potato (Solanum tuberosum L.), high temperature significantly reduces tuber anthocyanin pigment content. However, the mechanism of anthocyanin biosynthesis in potato tuber under heat stress remains unknown. Here we show that high temperature causes reduction of anthocyanin biosynthesis in both potato tuber skin and flesh, with white areas forming between the vasculature and periderm. Heat stress reduced the expression of the R2R3 MYB transcription factors (TFs) StAN1 and StbHLH1, members of the transcriptional complex responsible for coordinated regulation of the skin and flesh pigmentation, as well as anthocyanin biosynthetic pathway genes in white regions. However, the core phenylpropanoid pathway, lignin, and chlorogenic acid (CGA) pathway genes were up-regulated in white areas, suggesting that suppression of the anthocyanin branch may result in re-routing phenylpropanoid flux into the CGA or lignin biosynthesis branches. Two R2R3 MYB TFs, StMYB44-1 and StMYB44-2, were highly expressed in white regions under high temperature. In transient assays, StMYB44 represses anthocyanin accumulation in leaves of Nicotiana tabacum and N. benthamiana by directly suppressing the activity of the dihydroflavonol reductase (DFR) promoter. StMYB44-1 showed stronger repressive capacity than StMYB44-2, with both predicted proteins containing the repression-associated EAR motif with some variation. StMYB44-1 conferred repression without a requirement for a basic helix–loop–helix (bHLH) partner, suggesting a different repression mechanism from that of reported anthocyanin repressors. We propose that temperature-induced reduction of anthocyanin accumulation in potato flesh is caused by down-regulation of the activating anthocyanin regulatory complex, by enhancing the expression of flesh-specific StMYB44 and alteration of phenylpropanoid flux.
A cytorhabdovirus phosphoprotein forms mobile inclusions trafficked on the actin/ER network for viral RNA synthesis
Authors: Fang Xiao-Dong , Yan Teng , Gao Qiang , Cao Qing , Gao Dong-Min , Xu Wen-Ya , Zhang Zhen-Jia , Ding Zhi-Hang , Wang Xian-Bing 
Published: April 2019

AbstractAs obligate parasites, plant viruses usually hijack host cytoskeletons for replication and movement. Rhabdoviruses are enveloped, negative-stranded RNA viruses that infect vertebrates, invertebrates, and plants, but the mechanisms of intracellular trafficking of plant rhabdovirus proteins are largely unknown. Here, we used Barley yellow striate mosaic virus (BYSMV), a plant cytorhabdovirus, as a model to investigate the effects of the actin cytoskeleton on viral intracellular movement and viral RNA synthesis in a mini-replicon (MR) system. The BYSMV P protein forms mobile inclusion bodies that are trafficked along the actin/endoplasmic reticulum network, and recruit the N and L proteins into viroplasm-like structures. Deletion analysis showed that the N terminal region (aa 43–55) and the remaining region (aa 56–295) of BYSMV P are essential for the mobility and formation of inclusions, respectively. Overexpression of myosin XI-K tails completely abolishes the trafficking activity of P bodies, and is accompanied by a significant reduction of viral MR RNA synthesis. These results suggest that BYSMV P contributes to the formation and trafficking of viroplasm-like structures along the ER/actin network driven by myosin XI-K. Thus, rhabdovirus P appears to be a dynamic hub protein for efficient recruitment of viral proteins, thereby promoting viral RNA synthesis.
The effect of dust bias on the census of neutral gas and metals in the high-redshift Universe due to SDSS-II quasar colour selection
Authors: Krogager Jens-Kristian , Fynbo Johan P U , Møller Palle , Noterdaeme Pasquier , Heintz Kasper E , Pettini Max 
Published: April 2019

ABSTRACT
We present a systematic study of the impact of a dust bias on samples of damped Ly α absorbers (DLAs). This bias arises as an effect of the magnitude and colour criteria utilized in the Sloan Digital Sky Survey (SDSS) quasar target selection up until data release 7 (DR7). The bias has previously been quantified assuming only a contribution from the dust obscuration. In this work, we apply the full set of magnitude and colour criteria used up until SDSS-DR7 in order to quantify the full impact of dust biasing against dusty and metal-rich DLAs. We apply the quasar target selection algorithm on a modelled population of intrinsic colours, and by exploring the parameter space consisting of redshift, ($z_{\rm{\small QSO}}$and zabs), optical extinction, and H i column density, we demonstrate how the selection probability depends on these variables. We quantify the dust bias on the following properties derived for DLAs at z ≈ 3: the incidence rate, the mass density of neutral hydrogen and metals, and the average metallicity. We find that all quantities are significantly affected. When considering all uncertainties, the mass density of neutral hydrogen is underestimated by 10–50 per cent, and the mass density in metals is underestimated by 30–200 per cent. Lastly, we find that the bias depends on redshift. At redshift z = 2.2, the mass density of neutral hydrogen and metals might be underestimated by up to a factor of 2 and 5, respectively. Characterizing such a bias is crucial in order to accurately interpret and model the properties and metallicity evolution of absorption-selected galaxies.
Accurate prediction of boundaries of high resolution topologically associated domains (TADs) in fruit flies using deep learning
Authors: Henderson John , Ly Vi , Olichwier Shawn , Chainani Pranik , Liu Yu , Soibam Benjamin 
Published: April 2019

Abstract
Genomes are organized into self-interacting chromatin regions called topologically associated domains (TADs). A significant number of TAD boundaries are shared across multiple cell types and conserved across species. Disruption of TAD boundaries may affect the expression of nearby genes and could lead to several diseases. Even though detection of TAD boundaries is important and useful, there are experimental challenges in obtaining high resolution TAD locations. Here, we present computational prediction of TAD boundaries from high resolution Hi-C data in fruit flies. By extensive exploration and testing of several deep learning model architectures with hyperparameter optimization, we show that a unique deep learning model consisting of three convolution layers followed by a long short-term-memory layer achieves an accuracy of 96%. This outperforms feature-based models’ accuracy of 91% and an existing method's accuracy of 73–78% based on motif TRAP scores. Our method also detects previously reported motifs such as Beaf-32 that are enriched in TAD boundaries in fruit flies and also several unreported motifs.
Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2+
Authors: McCluskey Kaley , Boudreault Julien , St-Pierre Patrick , Perez-Gonzalez Cibran , Chauvier Adrien , Rizzi Adrien , Beauregard Pascale B , Lafontaine Daniel A , Penedo J Carlos 
Published: April 2019

Abstract
Riboswitches are cis-acting regulatory RNA biosensors that rival the efficiency of those found in proteins. At the heart of their regulatory function is the formation of a highly specific aptamer–ligand complex. Understanding how these RNAs recognize the ligand to regulate gene expression at physiological concentrations of Mg2+ ions and ligand is critical given their broad impact on bacterial gene expression and their potential as antibiotic targets. In this work, we used single-molecule FRET and biochemical techniques to demonstrate that Mg2+ ions act as fine-tuning elements of the amino acid-sensing lysC aptamer's ligand-free structure in the mesophile Bacillus subtilis. Mg2+ interactions with the aptamer produce encounter complexes with strikingly different sensitivities to the ligand in different, yet equally accessible, physiological ionic conditions. Our results demonstrate that the aptamer adapts its structure and folding landscape on a Mg2+-tunable scale to efficiently respond to changes in intracellular lysine of more than two orders of magnitude. The remarkable tunability of the lysC aptamer by sub-millimolar variations in the physiological concentration of Mg2+ ions suggests that some single-aptamer riboswitches have exploited the coupling of cellular levels of ligand and divalent metal ions to tightly control gene expression.
Ways to be Blameworthy
Authors: Mason Elinor 
Published: April 2019

Abstract
This book examines the relationship between our deontic notions, rightness and wrongness, and our responsibility notions, praise- and blameworthiness. The book presents a pluralistic view of both our deontic concepts and our responsibility concepts, identifying three different ways to be blameworthy. First, ordinary blameworthiness is essentially connected to subjective rightness and wrongness. Subjective obligation and ordinary blameworthiness apply only to those who are within our moral community, that is to say, those who understand and share our value system. By contrast, the second sort of blameworthiness, detached blameworthiness, can apply even when the agent is outside our moral community, and has no sense that her act is morally wrong. We blame agents for acting objectively wrongly, even if we do not have any view about their state of mind in so doing. Finally, the third sort of blameworthiness is ‘extended blameworthiness’, which applies in some contexts where the agent has acted wrongly, and understands the wrongness, but has acted wrongly entirely inadvertently. In such cases the agent is not personally at fault but the social context may be such that she should take responsibility, and thus become blameworthy.
Diversity of information sources: An evaluation of global think tanks knowledge construct
Authors: Ahmad Mahmood , Jan Muhammad Ayub 
Published: April 2019

AbstractIn the realm of policy making, place and prestige of think tanks is acknowledged for their contribution in policy analysis and recommendations. Governments around the world consider the reports and recommendations of leading global think tanks when developing their policies. However, in spite of there being a comprehensive list of typologies and functions of think tanks, much less is known about these ‘machineries of knowledge’ and what enables them ‘to know what they know, and the key sources of variation among them’. Drawing on the theory of epistemic knowledge, this study aims to provide insights about how knowledge is produced inside these machineries of knowledge by looking at source citations’ pattern of reports produced by the top 50 global think tanks. For this purpose, a total of 365 research reports on one country, i.e. Pakistan, published between 2007 and 2016 were retrieved. A total of 17,801 references were extracted and analyzed. The study finds that there is great variation across think tanks in the use of diverse information sources and the use also varies considerably over time even for the same organization.
Integrating Robotic Technology Into Resident Training: Challenges and Recommendations From the Front Lines
Authors: Green Courtney A. , Mahuron Kelly M. , Harris Hobart W. , O’Sullivan Patricia S. 
Published: April 2019

Purpose
To develop recommendations for improving the integration of robotic technology into today’s apprentice-based resident training.

Method
During a national meeting in 2017, 24 robotic surgeons were interviewed about their experiences integrating robotic technology into resident training. Qualitative thematic analysis of interview notes and recordings revealed themes related to challenges and recommendations.

Results
Four themes emerged, each corresponding to a general recommendation for integrating robotic technology into training. The first, surgical techniques versus tools, contrasts faculty’s sequential mastery—surgical techniques first, then the robotic tool—with residents’ simultaneous learning. The recommendation is to create separate learning opportunities for focused skill acquisition. The second theme, timing of exposure to the robotic tool, describes trainees’ initial focus on tool use for basic surgical steps. The recommendation is to increase access to basic robotic cases. The third theme covers the relationship of laparoscopic and robotic surgery. The recommendation is to emphasize similar and dissimilar features during all minimally invasive surgical cases. The fourth theme, use of the dual console (which enables two consoles to operate the robot, the primary determines the secondary’s functionality), highlights the unique teaching opportunities this console creates. The recommendation is for surgeons to give verbal guidance so residents completely understand surgical techniques.

Conclusions
Surgical educators should consider technique versus tool, timing of exposure to the tool, overlapping and varying features of robotic and laparoscopic surgery, and use of the dual console as they develop curricula to ensure thorough acquisition and synthesis of all elements of robotic surgery.