bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral Variants and Vaccinations: If We Can Change the COVID-19 Vaccine… Should We?
Authors: Bewick Sharon 
Published: January 2021

AbstractAs we close in on one year since the COVID-19 pandemic began, hope has been placed on bringing the virus under control through mass administration of recently developed vaccines. Unfortunately, newly emerged, fast-spreading strains of COVID-19 threaten to undermine progress by interfering with vaccine efficacy. While a long-term solution to this challenge would be to develop vaccines that simultaneously target multiple different COVID-19 variants, this approach faces both developmental and regulatory hurdles. A simpler option would be to switch the target of the current vaccine to better match the newest viral variant. I use a stochastic simulation to determine when it is better to target a newly emerged viral variant and when it is better to target the dominant but potentially less transmissible strain. My simulation results suggest that it is almost always better to target the faster spreading strain, even when the initial prevalence of this variant is much lower. In scenarios where targeting the slower spreading variant is best, all vaccination strategies perform relatively well, meaning that the choice of vaccination strategy has a small effect on public health outcomes. In scenarios where targeting the faster spreading variant is best, use of vaccines against the faster spreading viral variant can save many lives. My results provide ‘rule of thumb’ guidance for those making critical decisions about vaccine formulation over the coming months.
Glucocorticoid receptor activation induces gene-specific transcriptional memory and universally reversible changes in chromatin accessibility
Authors: Bothe Melissa , Buschow René , Meijsing Sebastiaan H. 
Published: January 2021

AbstractGlucocorticoids are stress hormones that elicit cellular responses by binding to the glucocorticoid receptor (GR), a ligand-activated transcription factor. The exposure of cells to this hormone induces wide-spread changes in the chromatin landscape and gene expression. Previous studies have suggested that some of these changes are reversible whereas others persist even when the hormone is no longer around. However, when we examined chromatin accessibility in human airway epithelial cells after hormone washout, we found that the hormone-induced changes were universally reversed after one day. Reversibility of hormone-induced changes are found for GR-occupied opening sites and also for closing sites that typically lack GR occupancy. These closing sites are enriched near repressed genes, suggesting that transcriptional repression by GR does not require nearby GR binding. Mirroring what we say in terms of chromatin accessibility, we found that transcriptional responses to hormone are universally reversable. Moreover, priming of cells by a previous exposure to hormone, in general, did not alter the transcriptional response to a subsequent encounter of the same cue. Interestingly, despite the short-lived nature of hormone-induced changes in the chromatin landscape, we identified a single gene,ZBTB16, that displays transcriptional memory manifesting itself as a more robust transcriptional response upon repeated hormone stimulation. Single-cell analysis revealed that the more robust response is driven by a higher probability of primed cells to activateZBTB16and by a subset of cells that express the gene at levels that are higher than the induction levels observed for naïve cells. Although our study shows that hormone-induced changes are typically reversable, exposure to hormone can induce gene-specific changes in the response to subsequent exposures which may play a role in habituation to stressors and changes in glucocorticoid sensitivity.
Distribution and diversity of dimetal-carboxylate halogenases in cyanobacteria
Authors: Eusebio Nadia , Rego Adriana , Glasser Nathaniel R. , Castelo-Branco Raquel , Balskus Emily P. , Leão Pedro N. 
Published: January 2021

AbstractHalogenation is a recurring feature in natural products, especially those from marine organisms. The selectivity with which halogenating enzymes act on their substrates renders halogenases interesting targets for biocatalyst development. Recently, CylC – the first predicted dimetal-carboxylate halogenase to be characterized – was shown to regio- and stereoselectively install a chlorine atom onto an unactivated carbon center during cylindrocyclophane biosynthesis. Homologs of CylC are also found in other characterized cyanobacterial secondary metabolite biosynthetic gene clusters. Due to its novelty in biological catalysis, selectivity and ability to perform C-H activation, this halogenase class is of considerable fundamental and applied interest. However, little is known regarding the diversity and distribution of these enzymes in bacteria. In this study, we used both genome mining and PCR-based screening to explore the genetic diversity and distribution of CylC homologs. While we found non-cyanobacterial homologs of these enzymes to be rare, we identified a large number of genes encoding CylC-like enzymes in publicly available cyanobacterial genomes and in our in-house culture collection of cyanobacteria. Genes encoding CylC homologs are widely distributed throughout the cyanobacterial tree of life, within biosynthetic gene clusters of distinct architectures. Their genomic contexts feature a variety of biosynthetic partners, including fatty-acid activation enzymes, type I or type III polyketide synthases, dialkylresorcinol-generating enzymes, monooxygenases or Rieske proteins. Our study also reveals that dimetal-carboxylate halogenases are among the most abundant types of halogenating enzymes in the phylum Cyanobacteria. This work will help to guide the search for new halogenating biocatalysts and natural product scaffolds.Data statementAll supporting data and methods have been provided within the article or through a Supplementary Material file, which includes 14 supplementary figures and 4 supplementary tables.
Animal linguistics: Exploring referentiality and compositionality in bird calls
Authors: Suzuki Toshitaka N. 
Published: January 2021

AbstractEstablishing the theory of language evolution is an ongoing challenge in science. One profitable approach in this regard is to seek the origins of linguistic capabilities by comparing language with the vocal communication systems of closely related relatives (i.e., the great apes). However, several key capabilities of language appear to be absent in non‐human primates, which limits the range of studies, such as direct phylogenetic comparison. A further informative approach lies in identifying convergent features in phylogenetically distant animals and conducting comparative studies. This approach is particularly useful with respect to establishing general rules for the evolution of linguistic capabilities. In this article, I review recent findings on linguistic capabilities in a passerine bird species, the Japanese tit (Parus minor). Field experiments have revealed that Japanese tits produce unique alarm calls when encountering predatory snakes, which serve to enhance the visual attention of call receivers with respect to snake‐like objects. Moreover, tits often combine discrete types of meaningful calls into fixed‐ordered sequences according to an ordering rule, conveying a compositional message to receivers. These findings indicate that two core capabilities of language, namely, referentiality and compositionality, have independently evolved in the avian lineage. I describe how these linguistic capabilities can be examined under field conditions and discuss how such research may contribute to exploring the origins and evolution of language.
Genome‐wide identification and analysis of sulfatase and sulfatase modifying factor genes in Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Ren Jun , Peng Zheng‐Ke , Yang Ze‐Zhong , Tian Li‐Xia , Liu Shao‐Nan , Wang Shao‐Li , Wu Qing‐Jun , Xie Wen , Zhang You‐Jun 
Published: January 2021

AbstractThe invasive pest whitefly (Bemisia tabaci) is a complex species, of which Middle East‐Minor Asia 1 (MEAM1) and Mediterranean (MED) are the two most damaging members. Previous research showed that cabbage is frequently infested with MEAM1 but seldomly with MED, and this difference in performance is associated with glucosinolate (GS) content. Some insects can modify GS using glucosinolate sulfatase (SULF), the activity of which is regulated by sulfatase modifying factor 1 (SUMF1); therefore, to increase our understanding of different performances of MEAM1 and MED on cabbage plants, we identified and compared nine putative SULFs and one SUMF in MEAM1 and MED. We found that the lengths of two genes, BtSulf2 and BtSulf4, differed between MEAM1 and MED. The messenger RNA levels of BtSulf4 increased more than 20‐fold after MEAM1 and MED adults were exposed to GS, but BtSulf2 expression was only induced by GS in MEAM1. Knockdown of BtSulf2 and BtSulf4 in MEAM1 resulted in a substantial increase in the mortality of GS‐treated adults but not in MED. These results indicate that differences in BtSulf2 and BtSulf4 sequences and/or expression may explain why MEAM1 performs better than MED on cabbage. Our results provide a basis for future functional research on SULF and SUMF in B. tabaci.
Collapsed
Authors: Pardue Derek 
Published: January 2021

SummaryAs part of a larger ethnographic project that approaches urban migration to São Paulo, Brazil as modes of racialized presence, I offer a fictionalized account of the tragic collapse of the Wilton Paes de Almeida Building (Fig. 1), an occupied, squatter settlement, on May 1, 2018. The narrative point of view represents the tension between the omniscient narrator and local actors, using an imaginative opening to examine migrant aspirations and fears. However, it is inescapably partial, its own kind of collapse. After the event, I was unable to locate the “real” people on which the characters were based. I did, however, revisit the area of destruction repeatedly and sat with the ruins (Fig. 2), the built environment playing its own role in memory and migrant experiences. The story follows Sembene, a Senegalese trader, his wife, Grace, and Flávio, a low‐level mafia operator, for twenty‐four hours leading up to and immediately following the collapse of building. We also glimpse their memories and longings as we move between their precarious residence in the building and a Senegalese commercial presence nearby. Ultimately, multiple collapses show the entangled forces of (il)legality, the urban, fortune, and belief in an understudied destination of contemporary African migration.
NGOs as Social Movements: Policy Narratives, Networks and the Performance of Dalit Rights in South India
Authors: Mosse David , Nagappan Sundara Babu 
Published: January 2021

ABSTRACTDonor‐funded development NGOs are sometimes portrayed as co‐opting, privatizing or depoliticizing citizen action or social movements. This much is implied by the term ‘NGOization’. Alternatively, NGOs can be seen as bearers of rights‐based work increasingly threatened by tighter regulation or substitution by corporate social responsibility models of development. This article engages critically with both perspectives. It traces the role of NGOs and their funders in agenda setting, specifically in bringing the previously excluded issue of caste discrimination into development policy discourse in the form of a Dalit‐rights approach in Tamil Nadu, south India. The authors explore the institutional processes of policy making and NGO networking involved, the alliances, entanglements of NGOs and social movements, and the performativity of NGO Dalit rights. But at the same time, the article illustrates how NGO institutional systems have constrained or failed to sustain such identity‐based claims to entitlement. In Nancy Fraser's terms, the article explores success and failure in addressing ‘first‐order’ issues of justice, that is rights to resources (in this case, land), and in tackling ‘second‐order’ injustices concerning the framing of who counts (who can make a claim as a rights holder) and how (by what procedures are claims and contests staged and resolved). This draws attention to the important but fragile achievements of NGOs’ discursive framings that give Dalits the ‘right to have rights’.
Point prevalence and motor function of children and adolescents with cerebral palsy in Scandinavia and Scotland: a CP‐North study
Authors: Hollung Sandra Julsen , Hägglund Gunnar , Gaston Mark S , Seid Abdu Kedir , Lydersen Stian , Alriksson‐Schmidt Ann I , Andersen Guro L 
Published: January 2021

AimTo describe the point prevalence of cerebral palsy (CP) and distribution of gross and fine motor function in individuals registered in a CP‐North surveillance programme.MethodAggregate data of individuals with CP aged 6 to 19 years, sex, CP subtype, and gross and fine motor function levels were collected from each programme. Overall and age‐specific point prevalence of CP was calculated for each programme using 95% confidence intervals. Logistic regression was used to estimate prevalence and CP subtypes with age as the covariate variable. Pearson χ2 tests were used to compare the distributions of CP subtypes, Gross Motor Function Classification System (GMFCS) levels, and Manual Ability Classification System (MACS) levels by age and between programmes.ResultsAmong 3 759 138 individuals residing in Scandinavia and Scotland, 8278 had a diagnosis of CP (57–59% were males). The overall point prevalence of CP ranged from 2.13 to 2.32 per 1000 residents. Age‐specific prevalence in each programme varied with the exception of Denmark. While the proportions of bilateral spastic CP were similar between programmes, there were variations in all other CP subtypes and in GMFCS and MACS levels.InterpretationWhile the results of this study may reflect real differences in CP populations between countries, they may not be clinically relevant. The variations may be attributable to differences in the year when each programme was first established, different data collection methods, and country‐specific governmental policies.
Psychometric properties of the Urdu version of the Geriatric Oral Health Assessment Index (GOHAI) and oral health‐related quality of life in the elder Pakistani population
Authors: Chaudhary Farooq Ahmad , Siddiqui Yasir Dilshad , Yaqoob Muhammad Azeem , Khalid Muhammad Danial , Butt Danial Qasim , Hameed Shoaib 
Published: January 2021

AbstractObjectiveThe study aimed to translate the English version of the Geriatric Oral Health Assessment Index, assess its reliability and validity, and demonstrate its psychometric properties with regard to OHRQoL in the elder Pakistani population.Material and methodsIn this cross‐sectional study, 408 elder people were randomly recruited from three day‐care centres. In the translation process, the translated Urdu version was reviewed by a committee of experts, followed by back‐translation into English and re‐reviewed by the same committee of experts. The questionnaire sought information about socio‐demographic characteristics information and self‐perception of oral, general health and treatment needs. OHRQoL was examined using GOHAI‐U, and intraoral examination recorded the decayed, missing, and filled teeth. Reliability, internal consistency, convergent and discriminant validity of GOHAI‐U were examined.ResultsThe mean GOHAI‐U score was 40.2 (SD = 5.7, range = 20‐55). The Cronbach's alpha for GOHAI score was 0.71, item‐scale correlation coefficients ranged from 0.63 to 0.76, and test–retest correlation ranged from 0.59 to 0.74. Three factors supported the theoretical construction in the component factor analysis of the index. For convergent validity, there was a significant relationship between the GOHAI score and self‐perceived oral, general health and treatment needs (P < .05). For discriminant validity, a significant correlation was found between the GOHAI score and clinical measures of dental health status except with the carious teeth.ConclusionThe GOHAI‐U has sufficient reliability and constructs validity to be used as an efficient measure of oral health‐related quality of life in the Pakistani elder population.
Efficacy of eradication therapy in Helicobacter pylori‐negative gastric mucosa‐associated lymphoid tissue lymphoma: A meta‐analysis
Authors: Jung Kyoungwon , Kim Do Hoon , Seo Hyun Il , Gong Eun Jeong , Bang Chang Seok 
Published: January 2021

AbstractBackground and AimsThe role of eradication therapy in Helicobacter pylori‐negative gastric mucosa‐associated lymphoid tissue (MALT) lymphoma remains controversial. The aim of this study was to investigate the efficacy of H. pylori eradication therapy as a first‐line treatment for H. pylori‐negative gastric MALT lymphoma.MethodsA literature search of studies published until October 2019 was performed using electronic databases. Studies that reported treatment response to eradication therapy as an initial treatment for patients with H. pylori‐negative gastric MALT lymphoma were eligible for inclusion. The primary outcome was the complete remission rate after eradication therapy.ResultsTwenty‐five studies were included in the analyses. The overall pooled complete remission rate was 29.3% (95% confidence interval [CI], 22.2%–37.4%, I2 = 41.5%). There was no publication bias, and the sensitivity analyses showed consistent results. The pooled complete remission rates were lower in the subgroups of studies that had a higher incidence of translocation t(11;18)(q21;q21) (19.9%, 95% CI, 11.6%–32.0%), studies that used serological tests to exclude H. pylori infection (27.5%, 95% CI, 20.1%–36.4%), and studies where non‐response to eradication therapy was determined at <12 months after treatment (27.0%, 95% CI, 15.5%–42.7%). Meta‐regression analysis revealed that the pooled estimate was not significantly different in terms of the characteristics of individual studies.ConclusionsAlthough the complete remission rate after eradication therapy is not high, it can be used as an initial treatment option in a subset of patients with H. pylori‐negative gastric MALT lymphoma. Further studies to identify subgroups of patients who may benefit from eradication therapy are needed.
AI‐2 represses CagA expression and bacterial adhesion, attenuating the Helicobacter pylori‐induced inflammatory response of gastric epithelial cells
Authors: Wen Yancheng , Huang Hongming , Tang Tiechen , Yang Huang , Wang Xi , Huang Xi , Gong Yingying , Zhang Xiaoyan , She Feifei 
Published: January 2021

AbstractBackgroundHelicobacter pylori (H. pylori) infection of gastric epithelial cells induces inflammatory response. Outer membrane proteins (OMPs), Type 4 secretion system (T4SS) encoded by cagPAI, and the effector protein CagA are involved in the pathogenesis of H. pylori. H. pylori possesses a gene encoding LuxS which synthesizes AI‐2, a quorum sensing signal molecule. The aim of this study was to investigate the role of AI‐2 in the expression of virulence factors and the inflammatory response of gastric epithelial (AGS) cells induced by H. pylori.Materials and MethodsH. pylori ΔluxS mutant was constructed, and AI‐2 activity was measured with Vibrio harveyi BB170. NF‐κB activation, IL‐8 production, expression of OMPs (outer membrane proteins), CagA, and T4SS encoded by cagPAI were investigated in H. pylori wild type, and ΔluxS with or without supplementation of AI‐2.ResultsH. pylori produced approximately 7 μM of AI‐2 in the medium. AI‐2 inhibited expression and translocation of CagA after infection of AGS cells. AI‐2 upregulated the expression of CagM, CagE, and CagX, while had no effect to the interaction between T4SS and α5β1 integrin. AI‐2 also reduced expression of adhesins and bacterial adhesion to AGS cells. Finally, AI‐2 reduced the activation of NF‐κB and expression of IL‐8 in H. pylori‐infected AGS.ConclusionsAI‐2 plays an important role in the pathogenesis of H. pylori. AI‐2 inhibits the bacterial adhesion, expression, and translocation of CagA, and attenuates the inflammatory response of AGS cells induced by H. pylori.
Fruit softening correlates with enzymatic activities and compositional changes in fruit cell wall during growing in Lycium barbarum L.
Authors: Liu Jun , Zhao Yuhui , Xu Hao , Zhao Xiaolu , Tan Yutian , Li Peipei , Li Dongdong , Tao Yingmei , Liu Dunhua 
Published: January 2021

SummaryThe present study aims to examine fruit cell wall‐associated fruit softening in Lycium barbarum L. by the microstructure of the fruit cells and the changes in the contents of cell wall components, molecular weights of cell wall polysaccharides and the activities of related cell wall degrading enzymes at different development stages of L. barbarum L. fruit. Fruit firmness significantly declined during ripening, with the greatest reduction between the 28 and 35 days stages. The decrease in firmness correlated with an extensively deformed microstructure in the parenchyma tissues and positively correlated with reductions in the contents of fruit cell wall materials and molecular weight in cell wall polysaccharide. Cellulase, α‐galactosidase, polygalactosidase and pectin methylesterase showed higher activities during 28 days; whereas, the activities of β‐galactosidase were higher during 35 days. These results indicate that cell wall‐related processes are a key feature of early softening in L. barbarum L.
Shared Standards versus Competitive Pressures in Journalism
Authors: Herzog Lisa 
Published: January 2021

AbstractDemocratic societies need media that uphold journalistic standards of truthfulness and objectivity. But sensationalism has always been a temptation for journalists, and given the intense competition between news outlets, especially in the online world, there is pressure on them to ‘chase the clicks’. The article analyzes the incentive structures for journalists – focusing on the harmfulness of sensationalist framing as an example – and the challenges of establishing shared standards in a highly competitive online environment. Drawing on concepts and arguments from business ethics, it argues that the structure of this problem points to the need for an ‘ethics of sportsmanship’ that upholds journalistic standards despite competitive pressures. But the specific role and nature of the media imply that there can be no once‐and‐for‐all solution. Instead, there is a need for reflexivity, that is, for an ongoing dialogue about journalistic standards and the role of media in democratic societies.