bluuebunny/crossref_metadata_2025 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

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.

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

Science 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

This 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

This 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

Graphs 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

We 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

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

The 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

In 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

In 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

The 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

Miscanthus, 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

Oxytocin (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

The 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.
Flow-diverting devices in the treatment of unruptured ophthalmic segment aneurysms at a mean clinical follow-up of 5 years
Authors: Kunert Przemysław , Wójtowicz Katarzyna , Żyłkowski Jarosław , Jaworski Maciej , Rabczenko Daniel , Wojciechowski Jakub , Leśniewski Kamil , Marchel Andrzej
Published: April 2021

A shift toward the endovascular treatment of ophthalmic segment aneurysms is noticeable. However, it is not clear if the long-term treatment results improve with the development of endovascular methods. The aim of this study was to present the outcomes of the treatment of unruptured ophthalmic aneurysms using flow diverting devices (FDD) with or without coiling. This retrospective study included 52 patients with 65 UIAs treated in 2009–2016. The mean aneurysm size was 8.8 mm. Eight aneurysms were symptomatic. Therapeutic procedures included: 5 failed attempts, 55 first sessions with FDD deployment (bilateral procedures in 3) and 3 retreatment procedures. To cover 55 ICAs, 25 Silk, 26 Pipeline, 9 Fred and 1 Surpass FDD were used. FDD with coiling was applied in 19(29.2%), mainly for symptomatic and larger aneurysms. Mean radiological and clinical follow-up was 12 and 61 months, respectively. Postprocedural deterioration was noted in 3(5.8%) patients, but in long-term the modified Rankin Scale grades 0–2 were achieved in 98.1% of patients. One patient died from the treated aneurysm rupture (annual risk—0.07%). Raymond–Roy occlusion classification class I or II was achieved in 98.5% in the long term, with similar results in both groups. Complications occurred in 40.4% of patients and the most frequent were: imperfect FDD deployment (15%), failed attempt of FDD deployment (9.6%) and late FDD stenosis (9.6%). Flow-diverting devices, with additional coiling in selected cases, may offer a very high proportion of satisfactory outcomes. However, in our experience the high risk of complications remains.
Exploring associations between constipation, severity of neurofibromatosis type 1 and NF1 mutational spectrum
Authors: Ejerskov Cecilie , Gaustadnes Mette , Ostergaard John R. , Krogh klaus , Thorsen Kasper , Borglum Anders D. , Haagerup Annette
Published: April 2021

Neurofibromatosis type 1 (NF1) is inherited in an autosomal dominant manner and is a rather common rare disease. Until recently, studies on gastrointestinal symptoms in patients with NF1 have been few and mostly described as case reports. In three previously published studies, the frequency of constipation in patients with NF1 has been found to be as high as 30%. In this study, associations between the frequency of constipation and NF1 disease severity and NF1 mutational spectrum were investigated. Among 277 patients with NF1, 49 had constipation. The highest rate of constipation was found among patients with a high perception of NF1 illness burden, and patients with constipation had a significantly higher NF1 illness burden when comparing the “not bothered” and the “very bothered” (p = 0.013). We found no significant association between constipation and the remaining measures on severity of NF1, nor between constipation and genetic variants. When observing the NF1 mutational spectrum, one variant (c.1013A>G (p.Asp338Gly/p.?) was identified in three patients with constipation of which two patients were related. The variant c.2970_2972delAAT (p.Met992del) associated with a mild NF1 phenotype was identified in two related patients with constipation. This study is the first to explore the association between symptoms of constipation, NF1 severity, and NF1 mutational spectrum. The results suggest an association between constipation and a high degree of illness burden. Awareness of this association among physicians could lead to more patients with NF1 being diagnosed with constipation. Constipation impacts on quality of life, hence a timely diagnosis and treatment will improve quality of life.
Evaluating the performance of multivariate indicators of resilience loss
Authors: Weinans Els , Quax Rick , van Nes Egbert H. , Leemput Ingrid A. van de
Published: April 2021

Various complex systems, such as the climate, ecosystems, and physical and mental health can show large shifts in response to small changes in their environment. These ‘tipping points’ are notoriously hard to predict based on trends. However, in the past 20 years several indicators pointing to a loss of resilience have been developed. These indicators use fluctuations in time series to detect critical slowing down preceding a tipping point. Most of the existing indicators are based on models of one-dimensional systems. However, complex systems generally consist of multiple interacting entities. Moreover, because of technological developments and wearables, multivariate time series are becoming increasingly available in different fields of science. In order to apply the framework of resilience indicators to multivariate time series, various extensions have been proposed. Not all multivariate indicators have been tested for the same types of systems and therefore a systematic comparison between the methods is lacking. Here, we evaluate the performance of the different multivariate indicators of resilience loss in different scenarios. We show that there is not one method outperforming the others. Instead, which method is best to use depends on the type of scenario the system is subject to. We propose a set of guidelines to help future users choose which multivariate indicator of resilience is best to use for their particular system.
Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress
Authors: Raghavendra K. P. , Das J. , Kumar R. , Gawande S. P. , Santosh H. B. , Sheeba J. A. , Kranthi S. , Kranthi K. R. , Waghmare V. N.
Published: April 2021

Asiatic cotton (Gossypium arboreum) cultivated as ‘desi cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X2-C-X17-H-X2-C)-X2-(C-X2-C-X17-C-X2-H)] and [(C-X2-C-X17-H-X2-C)-X2-(C-X4-C-X15-C-X2-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.
Psychosocial impact of Covid-19 outbreak on Italian asthmatic children and their mothers in a post lockdown scenario
Authors: Di Riso Daniela , Spaggiari Silvia , Cambrisi Elena , Ferraro Valentina , Carraro Silvia , Zanconato Stefania
Published: April 2021

Italy was the first European country to fight the Covid-19 outbreak. To limit the transmission of the virus, the Italian Government imposed strict domestic quarantine policies and temporary closure of non-essential businesses and schools from March 10th,2020. Although more and more literature is exploring the impact of the pandemic on non-referred children and families, only a few studies are focused on the psychosocial impact of Covid-19 in chronically ill children and their caregivers. The present study investigates asthma control and children and mothers’ psychological functioning (i.e.: psychological well-being, fear of contagion, and mothers’ Covid-19 related fears) in 45 asthmatic children aged 7-to-14, compared to a control sample. The subjects were administered an online survey after the lockdown (from 28th May to 23rd August 2020). The analysis shows that asthmatic children presented higher concern in relation to contagion, however, no difference in psychological functioning was displayed between the two cohorts. Mothers reported more Covid-19 related fears, and greater worries according to the resumption of their children’s activities. Moreover, they indicated a global worsening of their psychological well-being during the lockdown. Furthermore, regarding the clinical sample, the multivariate regression model showed that a worsening of mothers' psychological and children’s physical well-being was associated with a worsening of children’s psychological well-being during the lockdown. The results of this study indicate that mothers of asthmatic children can be more prone to experience psychological fatigue in a pandemic scenario. Special programs should be developed to support caregivers of chronically ill children.
The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion
Authors: Jeon Jong Yoon , Jung Ji-hwa , Suk Ho Young , Lee Hang , Min Mi-Sook
Published: April 2021

The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene.Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure ofK. koreanausing mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size ofK. koreanawas also small, these results suggest that the small, restricted populations ofK. koreanaare extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.
Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion
Authors: Plaper Tjaša , Aupič Jana , Dekleva Petra , Lapenta Fabio , Keber Mateja Manček , Jerala Roman , Benčina Mojca
Published: April 2021

Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
Immersion-plated palladium nanoparticles onto meso-porous silicon layer as novel SERS substrate for sensitive detection of imidacloprid pesticide
Authors: Al-Syadi A. M. , Faisal M. , Harraz Farid A. , Jalalah Mohammed , Alsaiari Mabkhoot
Published: April 2021

Herein, we demonstrate the effectiveness of surface-enhanced Raman scattering (SERS) to detect trace concentration of potentially harmful imidacloprid pesticide. To achieve this ultimate objective, a rapid and highly effective methodology for the fabrication of active and stable porous silicon (PSi) plated palladium nanoparticles (PdNPs) SERS substrates by an electrochemical anodization and immersion plating routes was applied. The PSi layers were fabricated by the electrochemical anodization of a silicon wafer in ethanoic fluoride solution, followed by uniformly deposition of PdNPs via a simple immersion plating technique. The structural features and morphology of fabricated frameworks of PSi-Pd NPs have been investigated by field emission scanning electron microscopy (FE-SEM) with energy dispersive X-ray (EDX), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) spectra. The PSi substrate demonstrates a meso-porous morphology with good distribution, good pore density and average pore sizes around 20 nm. The SERS performance of Si–Pd NPs and PSi–Pd NPs substrates has been examined taking imidacloprid (an insecticide) as a target analyte. The SERS signal of imidacloprid using PSi–Pd NPs substrate exhibited immense enhancement compared to the Si-Pd NPs substrate. The active substrate revealed excellent detectable performance with a concentration as low as 10–9 M imidacloprid and an enhancement factor (EF) of 1.2 × 105. This large EF is fundamentally ascribed to the combined effect of the electromagnetic improvement and charge transfer mechanisms. Additionally, no aging effect was observed for the present substrates kept in air for two weeks. Striking enhancement in Raman spectral signals obtained with the current PSi–Pd NPs substrates can provide a simple and smooth platform towards the sensitive detection of various target analytes.
Location and temporal memory of objects declines in aged marmosets (Callithrix jacchus)
Authors: De Castro Vanessa , Girard Pascal
Published: April 2021

Episodic memory decline is an early marker of cognitive aging in human. Although controversial in animals and called “episodic-like memory”, several models have been successfully developed, however they rarely focused on ageing. While marmoset is an emerging primate model in aging science, episodic-like memory has never been tested in this species and importantly in aged marmosets. Here, we examined if the recall of the what-when and what-where building blocks of episodic-like memory declines in ageing marmosets. We developed a naturalistic approach using spontaneous exploration of real objects by young and old marmosets in the home cage. We implemented a three-trial task with 1 week inter-trial interval. Two different sets of identical objects were presented in sample trials 1 and 2, respectively. For the test trial, two objects from each set were presented in a former position and two in a new one. We quantified the exploratory behaviour and calculated discrimination indices in a cohort of 20 marmosets. Young animals presented a preserved memory for combined what-where, and what-when components of the experiment, which declined with aging. These findings lead one to expect episodic-like memory deficits in aged marmosets.
Spin Seebeck effect of correlated magnetic molecules
Authors: Manaparambil Anand , Weymann Ireneusz
Published: April 2021

In this paper we investigate the spin-resolved thermoelectric properties of strongly correlated molecular junctions in the linear response regime. The magnetic molecule is modeled by a single orbital level to which the molecular core spin is attached by an exchange interaction. Using the numerical renormalization group method we analyze the behavior of the (spin) Seebeck effect, heat conductance and figure of merit for different model parameters of the molecule. We show that the thermopower strongly depends on the strength and type of the exchange interaction as well as the molecule’s magnetic anisotropy. When the molecule is coupled to ferromagnetic leads, the thermoelectric properties reveal an interplay between the spin-resolved tunneling processes and intrinsic magnetic properties of the molecule. Moreover, in the case of finite spin accumulation in the leads, the system exhibits the spin Seebeck effect. We demonstrate that a considerable spin Seebeck effect can develop when the molecule exhibits an easy-plane magnetic anisotropy, while the sign of the spin thermopower depends on the type and magnitude of the molecule’s exchange interaction.
‘Conjugate’ coseismic surface faulting related with the 29 December 2020, Mw 6.4, Petrinja earthquake (Sisak-Moslavina, Croatia)
Authors: Tondi Emanuele , Blumetti Anna Maria , Čičak Mišo , Di Manna Pio , Galli Paolo , Invernizzi Chiara , Mazzoli Stefano , Piccardi Luigi , Valentini Giorgio , Vittori Eutizio , Volatili Tiziano
Published: April 2021

We provide here a first-hand description of the coseismic surface effects caused by the Mw 6.4 Petrinja earthquake that hit central Croatia on 29 December 2020. This was one of the strongest seismic events that occurred in Croatia in the last two centuries. Field surveys in the epicentral area allowed us to observe and map primary coseismic effects, including geometry and kinematics of surface faulting, as well as secondary effects, such as liquefaction, sinkholes and landslides. The resulting dataset consists of homogeneous georeferenced records identifying 222 observation points, each of which contains a minimum of 5 to a maximum of 14 numeric and string fields of relevant information. The earthquake caused surface faulting defining a typical ‘conjugate’ fault pattern characterized by Y and X shears, tension cracks (T fractures), and compression structures (P shears) within a ca. 10 km wide (across strike), NW–SE striking right-lateral strike-slip shear zone (i.e., the Petrinja Fault Zone, PFZ). We believe that the results of the field survey provide fundamental information to improve the interpretation of seismological, GPS and InSAR data of this earthquake. Moreover, the data related to the surface faulting may impact future studies focused on earthquake processes in active strike-slip settings, integrating the estimates of slip amount and distribution in assessing the hazard associated with capable transcurrent faults.
Evaluation of digital dispense-assisted broth microdilution antimicrobial susceptibility testing for Pseudomonas aeruginosa isolates
Authors: Clark Shawn T. , Stapleton Patrick J. , Wang Pauline W. , Yau Yvonne C. W. , Waters Valerie J. , Hwang David M. , Guttman David S.
Published: April 2021

Antimicrobial susceptibility testing (AST) is essential for detecting resistance in Pseudomonas aeruginosa and other bacterial pathogens. Here we evaluated the performance of broth microdilution (BMD) panels created using a semi-automated liquid handler, the D300e Digital Dispenser (Tecan Group Ltd., CH) that relies on inkjet printing technology. Microtitre panels (96-well) containing nine twofold dilutions of 12 antimicrobials from five classes (β-lactams, β-lactam/β-lactamase inhibitors, aminoglycosides, fluoroquinolones, polymyxins) were prepared in parallel using the D300e Digital Dispenser and standard methods described by CLSI/ISO. To assess performance, panels were challenged with three well characterized quality control organisms and 100 clinical P. aeruginosa isolates. Traditional agreement and error measures were used for evaluation. Essential (EA) and categorical (CA) agreements were 92.7% and 98.0% respectively for P. aeruginosa isolates with evaluable on-scale results. The majority of minor errors that fell outside acceptable EA parameters (≥ ± 1 dilution, 1.9%) were seen with aztreonam (5%) and ceftazidime (4%), however all antimicrobials displayed acceptable performance in this situation. Differences in MIC were often log2 dilution lower for D300e dispensed panels. Major and very major errors were noted for aztreonam (2.6%) and cefepime (1.7%) respectively. The variable performance of D300e panels suggests that further testing is required to confirm their diagnostic utility for P. aeruginosa.
Tissue-specific regulatory mechanism of LncRNAs and methylation in sheep adipose and muscle induced by Allium mongolicum Regel extracts
Authors: Xue Jiangdong , Lv Qi , Khas Erdene , Bai Chen , Ma Bingjie , Li Wangjiao , Cao Qina , Fan Zejun , Ao Changjin
Published: April 2021

Allium mongolicum Regel (A. mongolicum) is a perennial and xerophytic Liliaceous allium plant in high altitude desert steppe and desert areas. Feeding A. mongolicum greatly reduced unpleasant mutton flavor and improves meat quality of sheep. We analyzed epigenetic regulatory mechanisms of water extracts of A. mongolicum (WEA) on sheep muscle and adipose using RNA-Seq and whole-genome Bisulfite sequencing. Feeding WEA reduced differentially expressed genes and long non-coding RNAs (lncRNAs) between two tissues but increased differentially methylation regions (DMRs). LncRNA and DMR targets were both involved in ATP binding, ubiquitin, protein kinase binding, regulation of cell proliferation, and related signaling pathways, but not unsaturated fatty acids metabolism. Besides, tissue specific targets were involved in distinct functional annotations, e.g., Golgi membrane and endoplasmic reticulum for muscle lncRNA, oxidative phosphorylation metabolism for adipose lncRNA, dsRNA binding for muscle DMRs. Epigenetic regulatory networks were also discovered to discovered essential co-regulated modules, e.g., co-regulated insulin secretion module (PDPK1, ATP1A2, CACNA1S and CAMK2D) in adipose. The results indicated that WEA induced distinct epigenetic regulation on muscle and adipose to diminish transcriptome differences between tissues, which highlights biological functions of A. mongolicum, tissue similarity and specificity, as well as regulatory mechanism of mutton odor.
Adulthood blood levels of hsa-miR-29b-3p associate with preterm birth and adult metabolic and cognitive health
Authors: Marttila Saara , Rovio Suvi , Mishra Pashupati P. , Seppälä Ilkka , Lyytikäinen Leo-Pekka , Juonala Markus , Waldenberger Melanie , Oksala Niku , Ala-Korpela Mika , Harville Emily , Hutri-Kähönen Nina , Kähönen Mika , Raitakari Olli , Lehtimäki Terho , Raitoharju Emma
Published: April 2021

Preterm birth (PTB) is associated with increased risk of type 2 diabetes and neurocognitive impairment later in life. We analyzed for the first time the associations of PTB with blood miRNA levels in adulthood. We also investigated the relationship of PTB associated miRNAs and adulthood phenotypes previously linked with premature birth. Blood MicroRNA profiling, genome-wide gene expression analysis, computer-based cognitive testing battery (CANTAB) and serum NMR metabolomics were performed for Young Finns Study subjects (aged 34–49 years, full-term n = 682, preterm n = 84). Preterm birth (vs. full-term) was associated with adulthood levels of hsa-miR-29b-3p in a fully adjusted regression model (p = 1.90 × 10–4, FDR = 0.046). The levels of hsa-miR-29b-3p were down-regulated in subjects with PTB with appropriate birthweight for gestational age (p = 0.002, fold change [FC] = − 1.20) and specifically in PTB subjects with small birthweight for gestational age (p = 0.095, FC = − 1.39) in comparison to individuals born full term. Hsa-miR-29b-3p levels correlated with the expressions of its target-mRNAs BCL11A and CS and the gene set analysis results indicated a target-mRNA driven association between hsa-miR-29b-3p levels and Alzheimer's disease, Parkinson's disease, Insulin signaling and Regulation of Actin Cytoskeleton pathway expression. The level of hsa-miR-29b-3p was directly associated with visual processing and sustained attention in CANTAB test and inversely associated with serum levels of VLDL subclass component and triglyceride levels. In conlcusion, adult blood levels of hsa-miR-29b-3p were lower in subjects born preterm. Hsa-miR-29b-3p associated with cognitive function and may be linked with adulthood morbidities in subjects born preterm, possibly through regulation of gene sets related to neurodegenerative diseases and insulin signaling as well as VLDL and triglyceride metabolism.