bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the contribution of osmotic and oxidative stress components on barley growth under salt stress
Authors: Nefissi Ouertani Rim , Abid Ghassen , Karmous Chahine , Ben Chikha Mariem , Boudaya Oumaima , Mahmoudi Henda , Mejri Samiha , Jansen Robert K , Ghorbel Abdelwahed 
Published: June 2021

Abstract
Salt stress is considered one of the most devastating environmental stresses, affecting barley growth and leading to significant yield loss. Hence, there is considerable interest in investigating the most effective traits that determine barley growth under salt stress. The objective of this study was to elucidate the contribution of osmotic and oxidative stress components in leaves and roots growth under salt stress. Two distinct barley (Hordeum vulgare) salt-stress tolerant genotypes, Barrage Malleg (BM, tolerant) and Saouef (Sf, sensitive), were subjected to 200 mM NaCl at early vegetative stages. Stressed and control leaves and roots tissue were assessed for several growth traits, including fresh and dry weight and plant length, as well as the content of osmoprotectants proline and soluble sugars. In addition, malondialdehyde content and activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX), as well as their corresponding gene expression patterns, were investigated. The results showed better performance of BM over Sf for leaf dry weight (LDW), root dry weight (RDW) and root length (RL). The salt-tolerant genotype (BM) had better osmoprotection against salt stress compared with the salt-sensitive genotype (Sf), with a higher accumulation of proline and soluble sugars in leaves and roots and a stronger antioxidant system as evidenced by higher activities of SOD, CAT and APX and more abundant Cu/Zn-SOD transcripts, especially in roots. Stepwise regression analysis indicated that under salt stress the most predominant trait of barley growth was Cu/Zn-SOD gene expression level, suggesting that alleviating oxidative stress and providing cell homeostasis is the first priority.
AQUARIUM: accurate quantification of circular isoforms using model-based strategy
Authors: Wen Guoxia , Li Musheng , Li Fuyu , Yang Zengyan , Zhou Tong , Gu Wanjun 
Published: June 2021

ABSTRACT

Summary
Currently, most computational methods estimate the expression of circular RNAs (circRNAs) using the number of sequencing reads that support back–splicing junctions (BSJ) in RNA-seq data, which may introduce biased estimation of circRNA expression due to the uneven distribution of sequencing reads. To overcome this, we previously developed a model-based strategy for circRNA quantification, enabling consideration of sequencing reads from the entire transcript. Yet, the lack of exact transcript structure of circRNAs may limit its accuracy. Here, we proposed a substantially improved circRNA quantification tool, AQUARIUM, by introducing the full-length RNA structure of circular isoforms. We assessed its performance in circRNA quantification using both biological and simulated rRNA-depleted RNA-seq datasets, and demonstrated its superior performance at both BSJ and isoform level.

Availability and implementation
AQUARIUM is freely available at https://github.com/wanjun-group-seu/AQUARIUM.

Supplementary information
Supplementary data are available at Bioinformatics online.
Application of ICH Guidelines for Studying the Degradation Behavior of Rocuronium Bromide Coupled with Stability-Indicating RP-LC Method
Authors: El Houssini Ola M , Abd El-Rahman Mohamed K , Fahem Diana K , Zaazaa Hala E 
Published: June 2021

Abstract
Non-depolarizing neuromuscular blocking agent Rocuronium bromide was quantified in drug substance and drug product using reversed-phase liquid chromatographic method. Forced degradation studies were conducted for Rocuronium bromide in drug substance under acidic (2MHCl), basic (2MNaOH), oxidative (3% H2O2), thermal (135°C) and photolytic (254 nm) stress conditions. An Agilent H12 C18 column was used for separation using diammonium hydrogen phosphate buffer (pH 8; 0.04M)- acetonitrile (50:50; v/v) as mobile phase at flow rate of 1 mL/min. The quantification was done using UV detection at 210 nm. The limit of quantification and detection was 11.1 and 3.66 μg/mL, respectively, and the recovery percentage was 99% in drug substance and drug product. ICH guidelines were adopted for method validation. The proposed LC method monitored the degradation profile for Rocuronium bromide under various stress conditions and provided a specific LC method for its routine analysis. Besides, the MS data were used to identify all Rocuronium bromide degradation products and the possible degradation pathway was designated.
Using fiction to engage audiences with infectious disease: the effect of the coronavirus pandemic on participation in the Bad Bugs Bookclub
Authors: Verran Joanna 
Published: June 2021

ABSTRACT
During Bad Bugs Bookclub meetings, scientists and non-scientists discuss novels in which infectious disease forms part of the plot in order to encourage public understanding of, and engagement with, microbiology. The website presents meeting reports and reading guides for over 70 novels. The aim of this work was to raise awareness of the bookclub and increase website engagement. In 2019, events designed to reach new audiences maintained an increase in page views from the end of 2018 (around 200 per month). In 2020, the coronavirus pandemic forced bookclub meetings online (Zoom). These, with podcasts and some Twitter discussion, increased page views with a peak of 400 per month. Membership increased, and global ‘attendance’ was facilitated. Feelings and observations related to each book and the pandemic were noted in meeting reports. A survey of current and previous bookclub members carried out early in lockdown with the aim of determining the future direction of the bookclub revealed the continuing value of both literary and scientific experiences to members. The bookclub has engaged scientists and non-scientists in meaningful discussion about infectious disease. Reach is modest, but the resource is significant, with potential impact in education and engagement.
Spectral element modeling of elastic wave propagation in an anisotropic background with discrete anisotropic fractures
Authors: Xu Jiaqi , Hu Hengshan , Liu Qing Huo , Zhan Qiwei , Zhuang Mingwei 
Published: June 2021

SUMMARY
We formulate and implement a spectral element method to simulate elastic wave propagation in an arbitrary anisotropic background with discrete anisotropic fractures. The approach uses a general linear-slip condition to incorporate the anisotropic fractures into SEM, which allows for discontinuities of displacement fields across the surfaces of fractures. We treat the extremely thin fractures as geometry interfaces instead of meshing them, thus reducing computational cost. The results obtained by the proposed method agree well with the reference solutions for both a single horizontal anisotropic planar fracture and a tilted fracture. Based on the numerical simulation, we analyse the effects of anisotropic fracture on the wavefields. We find that due to the presence of off-diagonal element in the anisotropic fracture stiffness matrix, the wavefields generated by the anisotropic fracture are different from the isotropic fracture. The method can also simulate the wavefields in the anisotropic background including the multiple fractures or the intersecting fractures.
Impact of gestational age on risk of cerebral palsy: unravelling the role of neonatal morbidity
Authors: Chen Ruoqing , Sjölander Arvid , Johansson Stefan , Lu Donghao , Razaz Neda , Tedroff Kristina , Villamor Eduardo , Cnattingius Sven 
Published: June 2021

Abstract

Background
The contribution of adverse consequences of preterm birth to gestational-age-related risk of cerebral palsy (CP) has rarely been studied. We aimed to assess the potential mediating roles of neonatal morbidity on the association between gestational age and risk of CP.

Methods
In this Swedish population-based study, 1 402 240 singletons born at 22–40 gestational weeks during 1998–2016 were followed from day 28 after birth for a CP diagnosis until 2017. Potential mediators included asphyxia, respiratory-related, infection-/inflammatory-related and neurological-related diseases within 0–27 days of life. Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). Causal mediation analysis was performed to estimate the proportion of the association mediated through pathways involving the four sequential mediators.

Results
We found an inverse dose–response relationship between gestational age and risk of CP, where the strongest association was observed for 22–24 weeks (HR 47.26, 95% CI 34.09–65.53) vs 39–40 weeks. Compared with non-diseased peers, children with neonatal morbidity, particularly those with neurological-related diseases (HR 31.34, 95% CI 26.39–37.21), had a higher risk of CP. The increased risk of CP was, at 24 weeks, almost entirely explained by neonatal morbidity (91.7%); this proportion decreased to 46.1% and 16.4% at 32 and 36 weeks, respectively. Asphyxia was the main mediating pathway from 22 to 34 weeks, and neurological-related neonatal diseases led the mediating pathways from 34 weeks onwards.

Conclusion
Neonatal morbidity mediates a large proportion of the effect of preterm birth on CP, but the magnitude declines as gestational age increases.
Time-Varying Association Between Severe Respiratory Syncytial Virus Infections and Subsequent Severe Asthma and Wheeze and Influences of Age at the Infection
Authors: Wang Xin , Li You , Nair Harish , Campbell Harry ,   RESCEU Investigators, Wang Xin , Reeves Rachel M , Li You , Campbell Harry , Nair Harish , van Wijhe Maarten , Kølsen Fischer Thea , Simonsen Lone , Trebbien Ramona , Tong Sabine , Bangert Mathieu , Demont Clarisse , Lehtonen Toni , University Hospital Turku , Heikkinen Terho , Teirlinck Anne , van Boven Michiel , van der Hoek Wim , van der Maas Nicoline , Meijer Adam , Vazquez Fernandez Liliana , Bøas Håkon , Bekkevold Terese , Flem Elmira , Stona Luca , Speltra Irene , Giaquinto Carlo , Cheret Arnaud , Leach Amanda , Stoszek Sonia , Beutels Philippe , Bont Louis , Pollard Andrew , Openshaw Peter , Abram Michael , Swanson Kena , Rosen Brian , Molero Eva 
Published: June 2021

Abstract

Background
Early-life severe respiratory syncytial virus (RSV) infection has been associated with subsequent risk of asthma and recurrent wheeze. However, changes in the association over time and the interaction effect of the age at first RSV infection are less well understood. We aimed to assess the time-varying association between RSV and subsequent asthma and wheeze admission and explore how the association was affected by the age at RSV infection.

Methods
We retrospectively followed up a cohort of 23 365 children for a median of 6.9 years using Scottish health databases. Children who were born between 2001 and 2013 and had RSV-associated respiratory tract infection (RTI) admissions under 2 years were in the exposed group; those with unintentional accident admissions under 2 years comprised the control group. The Cox proportional-hazards model was used to report adjusted hazard ratios (HRs) of RSV admissions on subsequent asthma and wheeze admissions. We did subgroup analyses by follow-up years. We also explored how this association was affected by the age at first RSV admission.

Results
The association was strongest in the first 2 years of follow-up and decreased over time. The association persisted for 6 years in children whose first RSV-RTI admission occurred at 6–23 months of age, with an adjusted HR of 3.9 (95% confidence interval [CI], 3.1–4.9) for the first 2 years, 2.3 (95% CI, 1.6–3.2) for 2 to &lt;4 years, and 1.9 (95% CI, 1.2–2.9) for 4 to &lt;6 years of follow-up. In contrast, the association was only significant for the first 2 years after first RSV-RTI admissions occurring at 0–5 months.

Conclusions
We found a more persistent association for subsequent asthma and wheeze in children whose first severe RSV infection occurred at 6–23 months compared to those whose first severe RSV infection occurred at 0–6 months. This provides new evidence for further assessment of the association and RSV intervention programs.
Molecular mechanism of MdWUS2–MdTCP12 interaction in mediating cytokinin signaling to control axillary bud outgrowth
Authors: Li Guofang , Tan Ming , Ma Juanjuan , Cheng Fang , Li Ke , Liu Xiaojie , Zhao Caiping , Zhang Dong , Xing Libo , Ren Xiaolin , Han Mingyu , An Na 
Published: June 2021

AbstractShoot branching is an important factor that influences the architecture of apple trees and cytokinin is known to promote axillary bud outgrowth. The cultivar ‘Fuji’, which is grown on ~75% of the apple-producing area in China, exhibits poor natural branching. The TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family genes BRANCHED1/2 (BRC1/2) are involved in integrating diverse factors that function locally to inhibit shoot branching; however, the molecular mechanism underlying the cytokinin-mediated promotion of branching that involves the repression of BRC1/2 remains unclear. In this study, we found that apple WUSCHEL2 (MdWUS2), which interacts with the co-repressor TOPLESS-RELATED9 (MdTPR9), is activated by cytokinin and regulates branching by inhibiting the activity of MdTCP12 (a BRC2 homolog). Overexpressing MdWUS2 in Arabidopsis or Nicotiana benthamiana resulted in enhanced branching. Overexpression of MdTCP12 inhibited axillary bud outgrowth in Arabidopsis, indicating that it contributes to the regulation of branching. In addition, we found that MdWUS2 interacted with MdTCP12 in vivo and in vitro and suppressed the ability of MdTCP12 to activate the transcription of its target gene, HOMEOBOX PROTEIN 53b (MdHB53b). Our results therefore suggest that MdWUS2 is involved in the cytokinin-mediated inhibition of MdTCP12 that controls bud outgrowth, and hence provide new insights into the regulation of shoot branching by cytokinin.
Quasi-essentiality of RNase Y inBacillus subtilisis caused by its critical role in the control of mRNA homeostasis
Authors: Benda Martin , Woelfel Simon , Faßhauer Patrick , Gunka Katrin , Klumpp Stefan , Poehlein Anja , Kálalová Debora , Šanderová Hana , Daniel Rolf , Krásný Libor , Stülke Jörg 
Published: June 2021

AbstractRNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
Demographics and Automation
Authors: Acemoglu Daron , Restrepo Pascual 
Published: June 2021

Abstract
We argue theoretically and document empirically that aging leads to greater (industrial) automation, because it creates a shortage of middle-aged workers specializing in manual production tasks. We show that demographic change is associated with greater adoption of robots and other automation technologies across countries and with more robotics-related activities across U.S. commuting zones. We also document more automation innovation in countries undergoing faster aging. Our directed technological change model predicts that the response of automation technologies to aging should be more pronounced in industries that rely more on middle-aged workers and those that present greater opportunities for automation and that productivity should improve and the labor share should decline relatively in industries that are more amenable to automation. The evidence supports all four of these predictions.
Distortions and Efficiency in Production Economies with Heterogeneous Beliefs
Authors: Heyerdahl-Larsen Christian , Walden Johan 
Published: June 2021

AbstractWe study consumption, savings, and asset prices in economies with disagreement and production, focusing on settings with real effects of disagreement. Aggregate savings may be significantly distorted under disagreement, possibly related to the undersaving puzzle. In the production economy, mispricing mainly manifests itself in idiosyncratic risk, in contrast to the exchange economy, where the risk-free rate and expected return on the market may be distorted. Potential policy implications include the introduction of investment taxes or subsidies. Our results highlight the real effects of disagreement in financial markets, and the differences between economies with and without production.
Illuminating the Proteasome: Fluorescence Assays for Investigating the Kinetics of Proteasome Substrate Processing
Authors: Bard Jared Abraham , Jonsson Erik , Martin Andreas 
Published: June 2021

Degradation of ubiquitinated substrates by the 26S proteasome is a tightly regulated multi‐step process. The 33 unique subunits of the proteasome must coordinate to bind the substrate's ubiquitin targeting signal, engage its unstructured region, translocate and unfold the polypeptide chain while concurrently removing the ubiquitin chains, and finally hydrolyze the peptide bonds. Many of the details of how the proteasome performs these tasks are still unknown. A better understanding of the timing and coordination of these events would provide critical insight into how the cell regulates the rate or extent of protein degradation by the proteasome.In order to gain molecular understanding of these processes, we have developed a fluorescent assay for directly studying the binding, engagement, and translocation of substrates by the heterohexameric AAA+ motor that feeds these substrates into the proteasome core for degradation. This was achieved by incorporating unnatural amino acids into the proteasome, which allowed for the site‐specific attachment of fluorescent dyes. Combined with previously developed tools for the heterologous expression, purification, and in‐vitro reconstitution of proteasome subcomplexes, this assay allows for a kinetic dissection of the substrate‐processing pathway. It will also allow us to test the effects of manipulating the substrate geometry or mutating proteasome components on the rate of individual processing steps. In addition to ensemble experiments, single‐molecule studies will reveal how individual processing events are timed and coordinated.Support or Funding InformationJ.B acknowledges support from the US National Science Foundation Graduate Research Fellowship. A.M. acknowledges support from the Searle Scholars Program, the US National Institutes of Health (grant R01‐GM094497), the US National Science Foundation CAREER Program (NSF‐MCB‐1150288), and A.M. and E.J. acknowledges support from the Howard Hughes Medical Institute.
Research for All: Large Introductory Laboratory Classes Investigate the Evolutionary Conservation of Metabolic Pathways
Authors: O'Connor Clare M. , Warner Douglas M. 
Published: June 2021

The explosion of genomic sequence information, particularly for microbial organisms, presents opportunities to engage large numbers of undergraduate students in authentic research within regular laboratory classes. The Pathways over Time project was designed as a semester‐long research investigation in which students investigate the phylogenetic conservation of enzymes involved in a metabolic pathway. The project was designed to teach students core concepts of molecular biology, including evolution, structure/function relationships, information transfer, energy transformation and systems biology. Other course goals include the application of the scientific process, quantitative analysis, and the use of databases and bioinformatics tools.Each semester, 150–200 students enroll in 12 parallel sections of BIOL2040, Investigations in Molecular Cell Biology. Working in teams of three, students study the conservation of enzymes involved in methionine biosynthesis between the budding yeast, S. cerevisiae, and the fission yeast, Schizosaccharomyces pombe, species separated by close to a billion years of evolution. Methionine biosynthesis in yeast involves several multi‐enzyme pathways, which are subject to a variety of regulatory controls. Working in teams of three, students become “experts” on one particular MET gene as they learn the basic techniques of microbiology, bioinformatics, molecular cell biology and genetics. The rapid pace of the course does not allow students to repeat experiments. Instead, students post their data to a data‐sharing wiki site to determine if their results are reproducible.Student learning is assessed with pre‐lab quizzes, lab notebooks, oral and poster presentations, database and literature assignments, and a series of “micro‐reports” that are assembled into a final research report in the format of a scientific publication. Pre‐and post‐course evaluation instruments include concept tests and self‐assessed confidence and learning gains. Assessment data indicate significant gains on all measures.The Pathways over Time project was designed with sustainability in mind. The project can be easily adapted to other organisms and enzyme systems, depending on instructor experience and interest. The three elements required for course design are a multi‐gene system to study, a genetically‐tractable organism for complementation analyses, and a test organism with a sequenced genome. At Boston College, for example, students have successfully demonstrated the conservation of multiple MET gene functions between S. cerevisiae and S. pombe. Moving forward, Boston College will use a new test organism in which MET gene function has been predicted from DNA sequence comparisons, but function has not been tested by complementation.Support or Funding InformationNational Science Foundation grant 114028