bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Arabidopsis thaliana mitochondria 5′ end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8
Authors: Schleicher Sarah , Binder Stefan 
Published: April 2021

Abstract
Key message
RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria.

Abstract
In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5′ termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5′ extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5′ end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5′ terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5′ end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5′ end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5′ end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5′ terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.
A Growing Body of Knowledge
Authors: Kersting Magdalena , Haglund Jesper , Steier Rolf 
Published: April 2021

AbstractScience deals with the world around us, and we understand, experience, and study this world through and with our bodies. While science educators have started to acknowledge the critical role of the body in science learning, approaches to conceptualising the body in science education vary greatly. Embodiment and embodied cognition serve as umbrella terms for different approaches to bodily learning processes. Unfortunately, researchers and educators often blur these different approaches and use various claims of embodiment interchangeably. Understanding and acknowledging the diversity of embodied perspectives strengthen arguments in science education research and allows realising the potential of embodied cognition in science education practice. We need a comprehensive overview of the various ways the body bears on science learning. With this paper, we wish to present such an overview by disentangling key ideas of embodiment and embodied cognition with a view towards science education. Drawing on the historical traditions of phenomenology and ecological psychology, we propose four senses of embodiment that conceptualise the body inphysical,phenomenological,ecological, andinteractionistterms. By illustrating the multiple senses of embodiment through examples from the recent science education literature, we show that embodied cognition bears on practical educational problems and has a variety of theoretical implications for science education. We hope that future work can recognise such different senses of embodiment and show how they might work together to strengthen the many roles of the body in science education research and practice.
Measuring Social Vulnerability in an Urban Space Through Multivariate Methods and Models
Authors: Davino Cristina , Gherghi Marco , Sorana Silvia , Vistocco Domenico 
Published: April 2021

AbstractThis article proposes a quantitative analysis to measure social vulnerability in a urban space, specifically in the area of the Municipality of Rome. Social vulnerability can be defined as a situation in which people are characterized by a condition of multidimensional deprivation that encompasses multiple aspects of life and exposes population to different risks and hazards produced by natural, environmental, socioeconomic and epidemic factors. The analysis that follows presents the use of multivariate methods and models to provide an index for every dimensions of vulnerability (housing quality, social context, education, employment, urban mobility, social relations and economic conditions) and a global index for mapping social vulnerability. The analysis also succeeds in identifying significant vulnerability spatial patterns and to measure how and if vulnerability can be different in case of an observed heterogeneity in urban space.
Evaluation of cement-bonded particleboards produced from mixed sawmill residues
Authors: Amiandamhen S. O. , Agwu C. U. , Ezenwaegbu P. N. 
Published: April 2021

AbstractThis study evaluates the application feasibility and properties of cement-bonded particleboards produced from mixed tropical hardwood species. Wood residues from a typical sawmill were collected, dried and used in the manufacturing of the cement composites. The wood residues used were fromCeiba pentandraandGmelina arboreatimber species. The residues were mixed in seven ratios in the production of the composite samples. Two control experimental samples containing unmixed residues of each species were also produced. The test carried out on the boards were flexural strength, water uptake properties and wet and dry screw withdrawal resistance. The effect of the wood mix ratio on the board properties was evaluated. The result showed that all properties except the screw withdrawal resistance were significantly influenced by the mix ratios (p < 0.05). The wet and dry screw withdrawal resistance ranged from 1170 to 1770 N and 1360 to 1830 N, respectively. The optimum wood mix ratio for enhancing mechanical performance of the boards was 1:4 ofC. pentandra/G. arboreawood residues. Based on the result of this study, the particleboards produced can be used as wood composite ceiling tiles in building applications.
Graph Learning for Combinatorial Optimization: A Survey of State-of-the-Art
Authors: Peng Yun , Choi Byron , Xu Jianliang 
Published: April 2021

AbstractGraphs have been widely used to represent complex data in many applications, such as e-commerce, social networks, and bioinformatics. Efficient and effective analysis of graph data is important for graph-based applications. However, most graph analysis tasks are combinatorial optimization (CO) problems, which are NP-hard. Recent studies have focused a lot on the potential of using machine learning (ML) to solve graph-based CO problems. Most recent methods follow the two-stage framework. The first stage is graph representation learning, which embeds the graphs into low-dimension vectors. The second stage uses machine learning to solve the CO problems using the embeddings of the graphs learned in the first stage. The works for the first stage can be classified into two categories, graph embedding methods and end-to-end learning methods. For graph embedding methods, the learning of the the embeddings of the graphs has its own objective, which may not rely on the CO problems to be solved. The CO problems are solved by independent downstream tasks. For end-to-end learning methods, the learning of the embeddings of the graphs does not have its own objective and is an intermediate step of the learning procedure of solving the CO problems. The works for the second stage can also be classified into two categories, non-autoregressive methods and autoregressive methods. Non-autoregressive methods predict a solution for a CO problem in one shot. A non-autoregressive method predicts a matrix that denotes the probability of each node/edge being a part of a solution of the CO problem. The solution can be computed from the matrix using search heuristics such as beam search. Autoregressive methods iteratively extend a partial solution step by step. At each step, an autoregressive method predicts a node/edge conditioned to current partial solution, which is used to its extension. In this survey, we provide a thorough overview of recent studies of the graph learning-based CO methods. The survey ends with several remarks on future research directions.
A replication of Pindyck’s willingness to pay: on the efforts required to obtain results
Authors: Gerotto Luca , Pellizzari Paolo 
Published: April 2021

AbstractWe replicate and use more recent data to re-estimate the paper “Uncertain outcomes and climate change policy”, Pindyck, J. Environ. Econ. Manag., 2012. In several cases, verification analysis confirms the results and the associated economic interpretation. However, those results cannot be replicated in one out of five cases. The replication is, therefore, only partially successful: the numerical results for some sets of parameter values turn out to be overly sensitive to a variety of technical computational settings. This suggests that great caution is needed with regard to estimates and policy conclusions based on this model. A re-estimation of the model using more recent climate data, which suggests that temperature increase is now higher on average but less widely dispersed, does not lead to significant economic differences in the results.
Innovative single-shot 2D pulse front tilt diagnostic
Authors: Galimberti M. , Bisesto F. G. , Galletti M. 
Published: April 2021

Abstract
The presence of pulse front tilt (PFT), caused by angular dispersion (AD) in femtosecond laser pulses, could degrade the performance of the laser system and/or impact the experimental yields. We present a single-shot diagnostic capable of measuring the AD in the x–y plane by adopting an intensity mask. It can be applied to stretched pulses, making it ideal for diagnosing the AD along the amplification chain of a high-power laser system, and to ultrashort pulses exiting from an optical compressor. In this way, it can help in properly characterizing a laser pulse before it is delivered to the target area. In this Letter, we present experimental evidence of AD retrieval for different compression configurations, supported by theoretical analysis.
Working memory and language aptitude in relation to listening strategy instruction in an instructed SLA context
Authors: Duman Saime Kara , Yalçın Şebnem , Erçetin Gülcan 
Published: April 2021

AbstractThe present small-scale study explores whether working memory (WM) and language aptitude (LA) explain any variance in L2 listening comprehension beyond baseline listening ability and explicit strategy-based listening instruction in an instructed EFL setting at the tertiary level. In a pretest/posttest non-randomized group design, the experimental group (N = 19) received explicit strategy-based listening instruction for 12 hours while the control group (N = 17) followed their regular L2 listening course syllabus. L2 listening comprehension was measured with an L2 academic listening comprehension test. WM measures (Foster et al., 2015) included an operation span task (OST), a symmetry span task (SST), and a rotation span task (RST). LA was assessed with LLAMA (Meara, 2005). The findings revealed the effectiveness of strategy-based intervention for L2 listening comprehension. A hierarchical regression analysis indicated that baseline listening scores explained about 52% of the variance in the post-listening scores, while listening strategy instruction explained an additional 16% of the variance. On the other hand, WM and LA did not explain any variance in listening comprehension scores, suggesting that the two individual learner differences in the present study are not significant predictors of L2 listening comprehension.
Urban agriculture: local government stakeholders’ perspectives and informational needs
Authors: Campbell Catherine G. , Rampold Shelli D. 
Published: April 2021

AbstractIn many US states, the power to regulate urban agriculture (UA) rests in local governments. Although there has been increased interest in UA, some local governments have been slow to adopt policies or ordinances to foster food production in urban areas or have actively sought to limit UA in their municipalities. To learn more about the disconnect between resident interest and local government policy, University of Florida, Institute of Food and Agricultural Sciences Extension and Center for Public Issues Education conducted a statewide survey of local government stakeholders (LGS) to assess their attitudes toward UA, subjective knowledge of UA, perceived benefits of and barriers to the implementation of UA and educational needs. Responses were collected using 5-point semantic differential and Likert-type scales. Overall, respondents displayed positive attitudes and moderate knowledge of UA, and they identified a number of benefits of and barriers to implementing UA in their communities. The findings of this study support the hypothesis that lack of basic knowledge about UA is one difficulty in fostering UA. Despite being positively disposed toward UA, LGS may not fully understand how to effectively develop and implement policies to foster UA. This finding may also help explain reluctance to adopt local government policies to support UA. Efforts to provide LGS key information and enhance their knowledge of UA may support the development of UA activities.
Inferring Ice Fabric From Birefringence Loss in Airborne Radargrams: Application to the Eastern Shear Margin of Thwaites Glacier, West Antarctica
Authors: Young T. J. , Schroeder D. M. , Jordan T. M. , Christoffersen P. , Tulaczyk S. M. , Culberg R. , Bienert N. L. 
Published: April 2021

AbstractIn airborne radargrams, undulating periodic patterns in amplitude that overprint traditional radiostratigraphic layering are occasionally observed, however, they have yet to be analyzed from a geophysical or glaciological perspective. We present evidence supported by theory that these depth‐periodic patterns are consistent with a modulation of the received radar power due to the birefringence of polar ice, and therefore indicate the presence of bulk fabric anisotropy. Here, we investigate the periodic component of birefringence‐induced radar power recorded in airborne radar data at the eastern shear margin of Thwaites Glacier and quantify the lateral variation in azimuthal fabric strength across this margin. We find the depth variability of birefringence periodicity crossing the shear margin to be a visual expression of its shear state and its development, which appears consistent with present‐day ice deformation. The morphology of the birefringent patterns is centered at the location of maximum shear and observed in all cross‐margin profiles, consistent with predictions of ice fabric when subjected to simple shear. The englacial fabric appears stronger inside the ice stream than outward of the shear margin. The detection of birefringent periodicity from non‐polarimetric radargrams presents a novel use of subsurface radar to constrain lateral variations in fabric strength, locate present and past shear margins, and characterize the deformation history of polar ice sheets.
Landscape Controls on Water‐Energy‐Carbon Fluxes Across Different Ecosystems During the North American Monsoon
Authors: Pérez‐Ruiz Eli R. , Vivoni Enrique R. , Yépez Enrico A. , Rodríguez Julio C. , Gochis David J. , Robles‐Morua Agustín , Delgado‐Balbuena Josué , Adams David K. 
Published: April 2021

AbstractThe dependence of arid and semiarid ecosystems on seasonal rainfall is not well understood when sites have access to groundwater. Gradients in terrain conditions in northwest México can help explore this dependence as different ecosystems experience rainfall during the North American monsoon (NAM), but can have variations in groundwater access as well as in soil and microclimatic conditions that depend on elevation. In this study, we analyze water‐energy‐carbon fluxes from eddy covariance (EC) systems deployed at three sites: a subtropical scrubland, a riparian mesquite woodland, and a mountain oak savanna to identify the relative roles of soil and microclimatic conditions and groundwater access. We place datasets during the NAM season of 2017 into a wider context using previous EC measurements, nearby rainfall data, and remotely‐sensed products. We then characterize differences in soil, vegetation, and meteorological variables; latent and sensible heat fluxes; and carbon budget components. We find that lower elevation ecosystems exhibited an intense and short greening period leading to a net carbon release, while the high elevation ecosystem showed an extensive water use strategy with delayed greening of longer duration leading to net carbon uptake during the NAM. Access to groundwater appears to reduce the dependence of deep‐rooted riparian trees at low elevation and mountain trees on seasonal rainfall, allowing for a lower water use efficiency as compared to subtropical scrublands sustained by water in shallow soils. Thus, a transition from intensive to extensive water use strategies can be expected where there is reliable access to groundwater.
Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome
Authors: Miao Jiashun , Feng Qi , Li Yan , Zhao Qiang , Zhou Congcong , Lu Hengyun , Fan Danlin , Yan Juan , Lu Yiqi , Tian Qilin , Li Wenjun , Weng Qijun , Zhang Lei , Zhao Yan , Huang Tao , Li Laigeng , Huang Xuehui , Sang Tao , Han Bin 
Published: April 2021

AbstractMiscanthus, a rhizomatous perennial plant, has great potential for bioenergy production for its high biomass and stress tolerance. We report a chromosome-scale assembly of Miscanthus lutarioriparius genome by combining Oxford Nanopore sequencing and Hi-C technologies. The 2.07-Gb assembly covers 96.64% of the genome, with contig N50 of 1.71 Mb. The centromere and telomere sequences are assembled for all 19 chromosomes and chromosome 10, respectively. Allotetraploid origin of the M. lutarioriparius is confirmed using centromeric satellite repeats. The tetraploid genome structure and several chromosomal rearrangements relative to sorghum are clearly demonstrated. Tandem duplicate genes of M. lutarioriparius are functional enriched not only in terms related to stress response, but cell wall biosynthesis. Gene families related to disease resistance, cell wall biosynthesis and metal ion transport are greatly expanded and evolved. The expansion of these families may be an important genomic basis for the enhancement of remarkable traits of M. lutarioriparius.
Universal nomenclature for oxytocin–vasotocin ligand and receptor families
Authors: Theofanopoulou Constantina , Gedman Gregory , Cahill James A. , Boeckx Cedric , Jarvis Erich D. 
Published: April 2021

AbstractOxytocin (OXT; hereafter OT) and arginine vasopressin or vasotocin (AVP or VT; hereafter VT) are neurotransmitter ligands that function through specific receptors to control diverse functions1,2. Here we performed genomic analyses on 35 species that span all major vertebrate lineages, including newly generated high-contiguity assemblies from the Vertebrate Genomes Project3,4. Our findings support the claim5 that OT (also known as OXT) and VT (also known as AVP) are adjacent paralogous genes that have resulted from a local duplication, which we infer was through DNA transposable elements near the origin of vertebrates and in which VT retained more of the parental sequence. We identified six major oxytocin–vasotocin receptors among vertebrates. We propose that all six of these receptors arose from a single receptor that was shared with the common ancestor of invertebrates, through a combination of whole-genome and large segmental duplications. We propose a universal nomenclature based on evolutionary relationships for the genes that encode these receptors, in which the genes are given the same orthologous names across vertebrates and paralogous names relative to each other. This nomenclature avoids confusion due to differential naming in the pre-genomic era and incomplete genome assemblies, furthers our understanding of the evolution of these genes, aids in the translation of findings across species and serves as a model for other gene families.
Evolutionary and biomedical insights from a marmoset diploid genome assembly
Authors: Yang Chentao , Zhou Yang , Marcus Stephanie , Formenti Giulio , Bergeron Lucie A. , Song Zhenzhen , Bi Xupeng , Bergman Juraj , Rousselle Marjolaine Marie C. , Zhou Chengran , Zhou Long , Deng Yuan , Fang Miaoquan , Xie Duo , Zhu Yuanzhen , Tan Shangjin , Mountcastle Jacquelyn , Haase Bettina , Balacco Jennifer , Wood Jonathan , Chow William , Rhie Arang , Pippel Martin , Fabiszak Margaret M. , Koren Sergey , Fedrigo Olivier , Freiwald Winrich A. , Howe Kerstin , Yang Huanming , Phillippy Adam M. , Schierup Mikkel Heide , Jarvis Erich D. , Zhang Guojie 
Published: April 2021

AbstractThe accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome—much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10−8 per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.