bluuebunny/crossref_metadata_2025 huggingface dataset:
The Right to Participate in the Life of the Society
Authors: Brownlee Kimberley
Published: October 2022

This chapter examines a specific category of rights—social participation rights—which include not only our rights to practise a faith in community with others, freedom of association, freedom of expression, and freedom of movement, but also an under-discussed set of rights: our interactional rights. The chapter shows that having access to ordinary, micro-moments of social connection with non-associates both underlies and partly constitutes our human right to participate in the life of the society. The chapter considers whether social participation rights are analogous to political participation rights and comments on specific barriers to social participation including segregation and loneliness. It concludes by addressing the objection that these rights are unclaimable.
Four Types of Anti-Loneliness Policies
Authors: de Vries Bouke
Published: October 2022

For many people, old age comes with an increased risk of loneliness as their social network shrinks and their capacity for rebuilding it is reduced due to the onset of age-related diseases and disabilities. As a large proportion of countries is ageing rapidly, this means that levels of loneliness (defined as a disutility-inducing mismatch between people’s desired relationships and their perceived realized relationships) are expected to rise. Yet despite this worrisome trend, few normative theorists have considered whether states have moral duties to address loneliness among (some of) their citizens and, if so, how they should do so. After suggesting that there are good reasons for thinking that many states have such duties, this chapter identifies four broad ways in they can help to prevent and alleviate loneliness.
Epilogue
Authors: Nickel James , Brownlee Kimberley
Published: October 2022

Someone who agrees that adequate social access is a human right, or at least a fundamental human interest, might still worry that, realistically, little can be done to realize this right or interest through individual, social, or political action. This Epilogue addresses this worry by identifying various feasible steps which can promote adequate social access today, including individual choices, social initiatives, and political efforts. The Epilogue focuses on potential bearers of responsibility including individuals themselves and families; civil society institutions such as religious, charitable, and business organizations; local, provincial, and national governments; and international legal and political institutions.
Knowing Science
Authors: Bird Alexander
Published: October 2022

Knowing Science presents an epistemology of science that rejects empiricism and gives a central place to the concept of knowledge. Science aims at knowledge and progresses when it adds to the stock of knowledge. That knowledge is social knowing—it is known by the scientific community as a whole. Evidence is that from which knowledge can be obtained by inference. From which it follows that evidence is knowledge. Evidence is not limited to perception, nor to observation. Observation supplies evidence that is basic relative to a field of enquiry and can be highly non-perceptual. Theoretical knowledge is typically gained by inference to the only explanation, in which competing plausible hypotheses are falsified by the evidence. In cases where not all competing hypotheses are refuted, scientific hypotheses are not known but possess varying degrees of plausibility. Plausibilities in the light of the evidence are probabilities and link eliminative explanationism to Bayesian conditionalization. Scientific realism and anti-realism are considered as metascientific claims. Such global metascientific claims are rejected—track records give us only local metascientific claims.
Silicon Palliates Chromium Toxicity through the Formation of Root Hairs in Rice (Oryza sativa) Mediated by GSH and IAA
Authors: Tripathi Durgesh Kumar , Rai Padmaja , Kandhol Nidhi , Kumar Alok , Sahi Shivendra , Corpas Francisco J , Sharma Shivesh , Singh Vijay Pratap
Published: October 2022

Along with the rapidly increasing environmental contamination by heavy metals, the exposure of plants to chromium has also magnified, resulting in a declined productivity. Hexavalent chromium [Cr(VI)], the most toxic form of Cr, brings about changes in plant processes at morpho-physiological and biochemical levels. However, silicon (Si) is known to mitigate the impact of abiotic stresses in plants. Here, we demonstrate Si-mediated alleviation of Cr(VI) toxicity and its effects on root hair formation in rice seedlings. Reduced glutathione (GSH) and indole-3 acetic acid (IAA, an important auxin) were assessed for their involvement in root hair formation after the application of Si to Cr(VI)-stressed plants, and our results confirmed their crucial significance in such developmental processes. The expression analysis of genes involved in GSH biosynthesis (OsGS2) and regeneration (OsGR1), and auxin biosynthesis (OsTAA1 and OsYUCCA1) and transport (OsAUX1 and OsPIN1) corroborated their positive role in Si-mediated root hair formation in Cr(VI)-stressed rice seedlings. Moreover, the results indicated that nitric oxide (NO) seems a probable but not fundamental component in Si-mediated formation of roots in rice during exposure to Cr(VI) stress. In this study, the indispensable role of GSH and IAA, redox homeostasis of GSH and IAA biosynthesis and transport are discussed with regard to Si-mediated formation of root hairs in rice under Cr(VI) stress. The results of the study suggest that Si is a protective agent against Cr(VI) stress in rice, and the findings can be used to develop Cr(VI) stress-tolerant varieties of rice with enhanced productivity.
Jellyfish diversity, trends and patterns in Southwestern Mediterranean Sea: a citizen science and field monitoring alliance
Authors: Gueroun Sonia K M , Piraino Stefano , KÉfi-Daly Yahia Ons , Daly Yahia Mohamed Néjib
Published: October 2022

Jellyfish (Cnidaria and Ctenophora) are an essential component of marine ecosystems and represent a potential effect, positive or negative, for several economic activities. Jellyfish blooms and non-indigenous species (NIS) introduction can shift ecological community structure and energy transfer. Despite their importance in ecosystem function and services, knowledge of jellyfish fauna diversity and phenology are largely lacking for the southern Mediterranean Sea. Here, we present an overview of the current state of jellyfish biodiversity in Tunisia. Based on a comprehensive literature survey, historical records and unpublished data, 66 jellyfish species, including 11 non-indigenous species, have been recorded in Tunisia between 1994 and 2020. Additionally, based on field surveys and a citizen science sighting program between 2004 and 2020, we present data on the spatial distribution of 13 conspicuous jellyfish taxa and the phenology of the eight most frequently detected species (Aurelia solida, Cotylorhiza tuberculata, Pelagia noctiluca, Phyllorhiza punctata, Rhizostoma pulmo, Rhopilema nomadica, Olindias muelleri and Velella velella) in Tunisian two ecoregions, the Western Mediterranean and the Tunisian Plateau. The 17 year survey showed a shift in R. pulmo, A. solida and P. noctiluca phenology. Additionally, citizen science revealed an increase in the spatial range of P. punctata (NIS) and the distinct phenologies of populations in the two ecoregions.
A stress-inducible protein regulates drought tolerance and flowering time in Brachypodium and Arabidopsis
Authors: Ying Sheng , Scheible Wolf-Rüdiger , Lundquist Peter Knut
Published: October 2022

To cope with environmental stresses and ensure maximal reproductive success, plants have developed strategies to adjust the timing of their transition to reproductive growth. This has a substantial impact on the stress resilience of crops and ultimately on agricultural productivity. Here, we report a previously uncharacterized, plant-specific gene family designated as Regulator of Flowering and Stress (RFS). Overexpression of the BdRFS gene in Brachypodium distachyon delayed flowering, increased biomass accumulation, and promoted drought tolerance, whereas clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout mutants exhibited opposite phenotypes. A double T-DNA insertional mutant in the two Arabidopsis (Arabidopsis thaliana) homologs replicated the effects on flowering and water deprivation seen in the B. distachyon CRISPR knockout lines, highlighting the functional conservation of the family between monocots and dicots. Lipid analysis of B. distachyon and Arabidopsis revealed that digalactosyldiacylglycerol (DGDG) and phosphatidylcholine (PC) contents were significantly, and reciprocally, altered in overexpressor and knockout mutants. Importantly, alteration of C16:0-containing PC, a Flowering Locus T-interacting lipid, associated with flowering phenotype, with elevated levels corresponding to earlier flowering. Co-immunoprecipitation analysis suggested that BdRFS interacts with phospholipase Dα1 as well as several other abscisic acid-related proteins. Furthermore, reduction of C18:3 fatty acids in DGDG corresponded with reduced jasmonic acid metabolites in CRISPR mutants. Collectively, we suggest that stress-inducible RFS proteins represent a regulatory component of lipid metabolism that impacts several agronomic traits of biotechnological importance.
Assessment and diagnosis of the acute hot joint: a systematic review and meta-analysis
Authors: Dey Mrinalini , Al-Attar Mariam , Peruffo Leticia , Coope Ashley , Zhao Sizheng Steven , Duffield Stephen , Goodson Nicola
Published: October 2022

Objectives

Prompt diagnosis of septic arthritis (SA) in acute native hot joints is essential for avoiding unnecessary antibiotics and hospital admissions. We evaluated the utility of synovial fluid (SF) and serum tests in differentiating causes of acute hot joints.

Methods

We performed a systematic literature review of diagnostic testing for acute hot joints. Articles were included if studying ≥1 serum or SF test(s) for an acute hot joint, compared with clinical assessment and SF microscopy and culture. English-language articles only were included, without date restriction. The following were recorded for each test, threshold and diagnosis: sensitivity, specificity, positive/negative predictive values and likelihood ratios. For directly comparable tests (i.e. identical fluid, test and threshold), bivariate random-effects meta-analysis was used to pool sensitivity, specificity, and areas under the curves.

Results

A total of 8443 articles were identified, and 49 were ultimately included. Information on 28 distinct markers in SF and serum, differentiating septic from non-septic joints, was extracted. Most had been tested at multiple diagnostic thresholds, yielding a total of 27 serum markers and 156 SF markers. Due to heterogeneity of study design, outcomes and thresholds, meta-analysis was possible for only eight SF tests, all differentiating septic from non-septic joints. Of these, leucocyte esterase had the highest pooled sensitivity [0.94 (0.70, 0.99)] with good pooled specificity [0.74 (0.67, 0.81)].

Conclusion

Our review demonstrates many single tests, individually with diagnostic utility but suboptimal accuracy for exclusion of native joint infection. A combination of several tests with or without a stratification score is required for optimizing rapid assessment of the hot joint.
Life is Too Short? Bereaved Managers and Investment Decisions
Authors: Liu Clark , Sulaeman Johan , Shu Tao , Yeung P Eric
Published: October 2022

We examine whether bereavement affects managerial investment decisions in large organizations using the exogenous events of managers’ family deaths. We find evidence that bereaved managers take less risk in separate samples of mutual funds and publicly traded firms. Mutual funds managed by bereaved managers exhibit smaller tracking errors, lower active share measures, and higher portfolio weights on larger stocks after bereavement events. Firms managed by bereaved CEOs exhibit lower capital expenditures and fewer acquisitions after bereavement events. Further analyses support the emotion-driven explanation over other explanations. The risk shifting by bereaved managers has negative implications on the performance of funds and firms that they manage.
Social cognitive processes explain bias in juror decisions
Authors: Castrellon Jaime J , Hakimi Shabnam , Parelman Jacob M , Yin Lun , Law Jonathan R , Skene Jesse A G , Ball David A , Malekpour Artemis , Beskind Donald H , Vidmar Neil , Pearson John M , Skene J H Pate , Carter R McKell
Published: October 2022

Jury decisions are among the most consequential social decisions in which bias plays a notable role. While courts take measures to reduce the influence of non-evidentiary factors, jurors may still incorporate biases into their decisions. One common bias, crime-type bias, is the extent to which the perceived strength of a prosecutor’s case depends on the severity of the crime. Moral judgment, affect and social cognition have been proposed as core processes underlying this and other biases. Behavioral evidence alone has been insufficient to distinguish these explanations. To identify the mechanism underlying crime-type bias, we collected functional magnetic resonance imaging patterns of brain activation from mock jurors reading criminal scenarios. Brain patterns from crime-type bias were most similar to those associated with social cognition (mentalizing and racial bias) but not affect or moral judgment. Our results support a central role for social cognition in juror decisions and suggest that crime-type bias and cultural bias may arise from similar mechanisms.
Disembodiment and Language in Schizophrenia: An Integrated Psychopathological and Evolutionary Perspective
Authors: Tonna Matteo , Lucarini Valeria , Borrelli Davide Fausto , Parmigiani Stefano , Marchesi Carlo
Published: October 2022

Different hypotheses have flourished to explain the evolutionary paradox of schizophrenia. In this contribution, we sought to illustrate how, in the schizophrenia spectrum, the concept of embodiment may underpin the phylogenetic and developmental pathways linking sensorimotor processes, the origin of human language, and the construction of a basic sense of the self. In particular, according to an embodied model of language, we suggest that the reuse of basic sensorimotor loops for language, while enabling the development of fully symbolic thought, has pushed the human brain close to the threshold of a severe disruption of self-embodiment processes, which are at the core of schizophrenia psychopathology. We adopted an inter-disciplinary approach (psychopathology, neuroscience, developmental biology) within an evolutionary framework, to gain an integrated, multi-perspectival model on the origin of schizophrenia vulnerability. A maladaptive over-expression of evolutionary-developmental trajectories toward language at the expense of embodiment processes would have led to the evolutionary “trade-off” of a hyper-symbolic activity to the detriment of a disembodied self. Therefore, schizophrenia psychopathology might be the cost of long-term co-evolutive interactions between brain and language.
A preliminary study of sleep spindles across non-rapid eye movement sleep stages in children with autism spectrum disorder
Authors: Kawahara Midori , Kagitani-Shimono Kuriko , Kato-Nishimura Kumi , Ohki Noboru , Tachibana Masaya , Kato Takafumi , Taniike Masako , Mohri Ikuko
Published: October 2022

Study Objectives

Sleep spindles play a crucial role in multiple neuronal network functions. Initiation and termination of spindles are regulated by the thalamic reticular nucleus and thalamocortical network, and the spindle can be an index for brain organization. We conducted a preliminary study of the parameters of sleep spindles, focusing on sleep-stage temporal distribution in children with autism spectrum disorder (ASD) with normal intelligence/developmental quotients.

Methods

We performed overnight polysomnography in 14 children with ASD (4–10 years) with normal full-scale intelligence quotient/developmental quotient (≥75) and 14 community samples (CS) of children. Sleep stages were scored according to the Rechtschaffen and Kales criteria. Spindle parameters were quantified and compared between these groups and the identified subgroups.

Results

Sleep parameters did not differ between the ASD and CS groups, except for a higher rate of rapid eye movement (REM) sleep duration in ASD. Spindle parameters did not significantly differ between the groups, but spindle density was distributed in a broader range in the ASD group. Five children with ASD had a higher spindle density in stage 3 than in stage 2. The ratio of spindle density in stage 3 to that in stage 2 (stage 3/2 ratio) was significantly higher in ASD than in CS cases.

Conclusions

The lower spindle density in stage 2 and relatively higher density in stage 3 in children with ASD may represent an abnormal generation of spindles due to insufficient maturation of the thalamic reticular nucleus and thalamocortical network.
An endophytic fungus,Piriformospora indica, enhances drought tolerance of trifoliate orange by modulating the antioxidant defense system and composition of fatty acids
Authors: Cao Jin-Li , He Wan-Xia , Zou Ying-Ning , Wu Qiang-Sheng
Published: October 2022

A cultivable endophytic fungus, Piriformospora indica, improves growth and enhances stress tolerance of host plants, but the underlying mechanisms remain unknown. We hypothesized that P. indica enhanced the drought tolerance of the host by regulating the antioxidant defense system and composition of fatty acids. Trifoliate orange (Poncirus trifoliata) seedlings were inoculated with P. indica under ample water and drought stress to analyze the change in plant growth, reactive oxygen species (ROS) levels, antioxidant enzyme activities, non-enzymatic antioxidant concentrations, fatty acid compositions, and expressions of both antioxidant enzyme genes and fatty acid desaturase (FAD) genes. The 9-week soil water deficit significantly increased the colonization of P. indica to roots, and P. indica promoted the increase of shoot biomass under drought. Soil drought triggered an elevation of hydrogen peroxide in roots, while the inoculated plants had lower levels of ROS (hydrogen peroxide and superoxide anion radicals) and lower degree of membrane lipid peroxidation (based on malondialdehyde levels) under drought. Drought treatment also elevated ascorbic acid and glutathione concentrations, and the elevation was further amplified after P. indica inoculation. Inoculated plants under drought also recorded significantly higher iron-superoxide dismutase (Fe-SOD), manganese-superoxide dismutase (Mn-SOD), peroxidases, catalase, glutathione reductase and ascorbate peroxidase activities, accompanied by up-regulation of PtFe-SOD and PtCu/Zn-SOD expressions. Inoculation with P. indica significantly increased total saturated fatty acids (e.g., C6:0, C15:0, C16:0, C23:0 and C24:0) concentration and reduced total unsaturated fatty acids (e.g., C18:1N9C, C18:2N6, C18:3N3, C18:1N12 and C19:1N9T) concentrations, leading to a decrease in the unsaturation index of fatty acids, which may be associated with the up-regulation of PtFAD2 and PtFAD6 and down-regulation of PtΔ9. It was concluded that the colonization of P. indica can activate enzyme and non-enzyme defense systems and regulate the composition of fatty acids under drought, thus alleviating the oxidative damage to the host caused by drought.
False-positive fourth-generation HIV test result in a woman with Plasmodium malariae malaria
Authors: Ainoda Yusuke , Komaki-Yasuda Kanako , Kano Shigeyuki , Hirai Yuji
Published: October 2022

Background

False positive results on fourth-generation human immunodeficiency virus (HIV) diagnostic tests have previously been reported in infections with Plasmodium falciparum and Plasmodium ovale but not with Plasmodium malariae.

Methods

We report a false positive fourth-generation HIV test result in a patient with P. malariae infection. The patient's symptoms improved rapidly with antimalarial treatment and the confirmatory and repeated HIV tests were eventually negative.

Results

False positive results may add a variety of unnecessary burden.

Conclusions

One must be aware of false positive results even with fourth-generation tests in patients with malaria, including P. malariae malaria.
Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Authors: Pelegrin Jonathan S , Cantalapiedra Juan L , Gamboa Sara , Menéndez Iris , Hernández Fernández Manuel
Published: October 2022

Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for the first time, the evolution of biome occupation in birds. We aimed to analyse patterns of adaptation to different climatic regimes and the determinant factors for colonization of emerging biomes by clades from different ancestral biomes. In this work, we reconstructed the biome occupation history of two clades of birds (Galliformes and Falconiformes) under an integrative perspective through a comprehensive review of ecological, phylogenetic, palaeontological and biogeographical evidence. Our findings for both groups are consistent with a scenario of phylogenetic biome conservatism and highlight the importance of changes in climate during the Miocene in the adaptation and evolution of climatic niches. In particular, our results indicate high biome conservatism associated with biomes situated in some of the extremes of the global climate gradient (evergreen tropical rainforest, steppe and tundra) for both bird taxa. Finally, the historical dynamics of tropical seasonal biomes, such as tropical deciduous woodlands and savannas, appear to have played a preponderant role during the diversification processes of these bird lineages.
Whole-Genome Sequencing of Fusarium oxysporum f. sp. cucumerinum Strain Race-4 Infecting Cucumber in China
Authors: Yang Jingjing , Mao Aijun , Zhang Jian , Zhang Xiaofei , Xia Changxuan , Zhao Hong , Wang Yixin , Wen Changlong , Liu Hui , Wang Qian
Published: October 2022

Fusarium oxysporum f. sp. cucumerinum, which causes root and vascular wilting, is one of the most devastating diseases infecting cucumber. Here, we report the first genome resource with high-quality assembly for F. oxysporum f. sp. cucumerinum strain Race-4, which is primarily endemic to China. The genome was 59.11 Mb in size and consisted of 48 scaffolds with an N50 of 3.87 Mb using PacBio long reads (301.77×) sequencing, and encodes 14,898 proteins from analyzing RNA-seq data. Gene annotations identified pathogen-host interaction genes, fungal virulence factors, secreted proteins, transcription factors, and secondary metabolite biosynthesis gene. Moreover, functional genes reported in previous studies were also identified in the genome of Race-4. These genes and genome resource may play important roles in understanding F. oxysporum f. sp. cucumerinum–cucumber interactions and will be useful for further research.
Evidence for Vector Transmission of the Blueberry Pathogen Exobasidium maculosum, Cause of Exobasidium Leaf and Fruit Spot
Authors: Newell Annakay D. , Sial Ashfaq A. , Brewer Marin T.
Published: October 2022

Exobasidium leaf and fruit spot of blueberry, caused by Exobasidium maculosum, results in significant yield losses if not properly managed. To determine if an arthropod is involved in transmission, we conducted arthropod exclusion and trapping studies at two field sites in Georgia from 2018 to 2020. In each field, 10 pairs of potted trap plants were placed under blueberry bushes for 2 weeks during the known infection window in early spring. In each pair, one potted plant was covered with exclusion nets before being taken to the field, and the other was left uncovered. The covered plants developed significantly fewer leaf spots (mean = 2) than the uncovered plants (mean = 128), indicating that an agent necessary for infection was excluded. To identify possible vectors, a variety of traps were used to collect arthropods in both fields during the known infection window. A total of 181 insects were selected from traps, then crushed and plated on potato dextrose agar to assess for growth of E. maculosum. A species-specific PCR assay was developed and conducted to test for E. maculosum. We recovered E. maculosum from one gall midge (Diptera: Cecidomyiidae) and detected it in three additional insects by PCR. One could not be identified, and two were two long-legged flies (Diptera: Dolichopodidae). Bioassays with spotted-wing drosophila ( Drosophila suzukii) and brown marmorated stink bugs ( Halyomorpha halys) did not show transmission of the disease. Although we did not conclusively identify specific vectors, we provide evidence of vector involvement in transmission of E. maculosum.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Peer Reviewing Papers for a Nursing Journal
Authors: Pierson Charon A.
Published: October 2022

Editors rely on peer reviewers' comments and insight as they make decisions about submitted manuscripts. This article describes what reviewers need to consider when accepting a peer review assignment and the essential elements they should include in their peer review.
Antibiotic Stewardship Program Reduces Use of Urine Cultures and Antibiotics for Asymptomatic Bacteriuria
Authors: Rosenberg Karen
Published: October 2022

According to this study:

An individualized intervention for antibiotic stewardship in patients who had asymptomatic bacteriuria was associated with a reduction in the number of orders for urine cultures and use of antibiotics.
A tissue injury repair pathway distinct but parallel to host pathogen defense
Authors: Liu Siqi , Hur Yun Ha , Cai Xin , Cong Qian , Yang Yihao , Xu Chiwei , Bilate Angelina M. , Uy Gonzales Kevin Andrew , Cowley Christopher J. , Hurwitz Brian , Luo Ji-Dung , Tseng Tiffany , Gur-Cohen Shiri , Sribour Megan , Omelchenko Tatiana , Levorse John , Pasolli Hilda Amalia , Thompson Craig B. , Mucida Daniel , Fuchs Elaine
Published: October 2022

Pathogen infection and tissue injury are universal insults that disrupt homeostasis. Innate immunity senses microbial infections and induces interferons (IFNs) to activate resistance mechanisms. Applying unbiased phylogenetic analysis, we show that interleukin-24 (IL24) is among the closest evolutionary homologs to the IFN family and shares a common ancestral origin. However, in contrast to IFNs, IL24 induction occurs specifically in barrier epithelial progenitors after injury and is independent of microbiome or adaptive immunity. Surprisingly,Il24ablation impedes not only epidermal proliferation and re-epithelialization, but also capillary and fibroblast regeneration within the dermal wound bed. Conversely, ectopicIl24 induction in homeostatic epidermis triggers global epithelial-mesenchymal tissue repair responses. Mechanistically, sustainedIl24expression depends upon both IL24 receptor/STAT3 signaling and also hypoxia-stabilized HIF1α, which converge following injury. Thus, parallel to the IFN-mediated innate immune sensing of pathogens to resolve infections, epithelial stem cells sense injury signals to orchestrate IL24-mediated tissue repair.
The humoral and cellular immune response of a third dose adenoviral-based vectored vaccine after a single or 2 shots of inactivated COVID-19 vaccine in healthy adults
Authors: Suparak Supaporn , Bumroongthai Kobkaew , Jantapalaboon Danai , Pairoung Phanapat , Wongkidakarn Sudarat , Yodtub Chonlada , Puangtubtim Wiroj , Pimpapai Warangluk , Soonthorncharttrawat Sakulrat , Dhepaksorn Panadda , Mahasirimongkol Surakameth
Published: October 2022

The coronavirus pandemic is a severe infectious respiratory disease which caused massive loss worldwide. Thailand was affected by the wild-type, and the Delta variant started in mid-2021. Due to the shortage of effective vaccines, the ministry of public health of Thailand suggested the heterologous vaccine scheme, which comprises inactivated COVID-19 vaccine (CoronaVac) and an adenoviral-based vectored vaccine (ChAdOx1). However, data on the humoral and cellular immune responses of the single or 2 shots of inactivated vaccine followed by the adenoviral-based vaccine are very limited. In this current study, the sera from participants who received either single or 2 shots of CoronaVac followed by the ChAdOx1 vaccine were evaluated for SARS-CoV-2 spike receptor-binding-domain (RBD) IgG. The cytokine level was also assessed using Luminex immunoassay. The PBMC were collected to evaluate spike-specific T-cell and B-cell responses. Participants who received 2 shots of CoronaVac followed by ChAdOx1 possessed significantly (P<0.0001) higher levels of spike RBD-specific IgG. They also exhibited a higher level of CD4+T-cell and IFN-gamma than those who received only 1 shot of CoronaVac followed by the ChAdOx1 vaccine. The volunteers who received two shots of CoronaVac followed by ChAdOx1 had a significantly (p<0.01) higher marginal B-cell response against wild-type SARS-CoV-2 S peptides than those who received only one shot of CoronaVac followed by ChAdOx1. Surprisingly, the class switch B-cell response to Delta variant SARS-CoV-2 S peptides of the volunteers who received 1 shot of CoronaVac followed by ChAdOx1 was significantly (p<0.01) higher than those who received 2 shots of CoronaVac. However, participants who received only a single shot of inactivated vaccine followed by an adenoviral-based vectored vaccine possessed a higher level of TNF-alpha and IL-6. This study indicated that boosting the ChAdOx1 as a third dose after completing 2 shots of CoronaVac induced strong humoral and cellular immune responses.
NlpE is an OmpA-associated outer membrane sensor of the Cpx envelope stress response
Authors: Cho Timothy H. S. , Wang Junshu , Raivio Tracy L.
Published: October 2022

Gram-negative bacteria utilize several envelope stress responses (ESRs) to sense and respond to diverse signals within a multi-layered cell envelope. The CpxRA ESR responds to multiple stresses that perturb envelope protein homeostasis. Signaling in the Cpx response is regulated by auxiliary factors such as the outer membrane (OM) lipoprotein NlpE, an activator of the response. NlpE communicates adhesion to surfaces to the Cpx response; however, the mechanism by which NlpE accomplishes this remains unknown. In this study, we report a novel interaction between NlpE and the abundant OM protein OmpA. Both NlpE and OmpA are required to activate the Cpx response in surface-adhered cells. Furthermore, NlpE senses OmpA overexpression and the NlpE C-terminal domain transduces this signal to the Cpx response, revealing a novel signaling function for this domain. Overall, these findings reveal NlpE to be a versatile envelope sensor that takes advantage of its structure, localization, and cooperation with other envelope proteins to initiate adaptation to diverse signals.

Significance

The envelope is not only a barrier that protects bacteria from the environment but also a crucial site for the transduction of signals critical for colonization and pathogenesis. The discovery of novel complexes between NlpE and OmpA contributes to an emerging understanding of the key contribution of complexes of β-barrel proteins and lipoproteins to envelope stress signaling. Overall, our findings provide mechanistic insight into how the Cpx response senses signals relevant to surface adhesion and biofilm growth to facilitate bacterial adaptation.
Did variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?
Authors: Zhou Zijun , Swagemakers Sigrid M.A , Lourens Mirthe S. , Suratannon Narissara , van der Spek Peter J. , Dalm Virgil A.S.H. , Dik Willem A. , IJspeert Hanna , van Hagen P. Martin
Published: October 2022

Neanderthals were a species of archaic human that became extinct around 40,000 years ago. Modern humans have inherited 1-6% of Neanderthal DNA as a result of interbreeding with the Neanderthals. These inherited Neanderthal genes have paradoxical influences, while some can provide protection to viral infections, some others are associated with autoimmune/auto-inflammatory diseases.

We hypothesized that genetic variants with strong detrimental effects on the function of the immune system could potentially contributed to the extinction of the Neanderthal population. In modern humans more than 450 genes are associated with inborn errors of immunity (IEI). We used the publically available genome information from a Neanderthal from the Altai mountains and filtered for potentially damaging variants that were present in genes associated with IEI, and checked whether these variants were present in the genomes of the Denisovan, Vindija and Chagyrskaya Neanderthals.

We identified 24 homozygous variants and 15 heterozygous variants in IEI-related genes in the Altai Neanderthal. Interestingly, two homozygous variants in theUNC13Dgene and one variant in theMOGSgene were present in all archaic genomes. Defects in theUNC13Dgene are known to cause a severe and often fatal disease called hemophagocytic lymphohistiocystosis (HLH). One of these variants p.(Asn943Ser) has been reported in patients with HLH. Variants inMOGSare associated with glycosylation defects in the immune system affecting the susceptibility for infections. So, although we do not know exactly the functional impact yet, these three variants could have resulted in an increased susceptibility to severe diseases, and may have contributed to the extinction of Neanderthals after exposure to specific infections.
dnaE2expression promotes genetic diversity and bacterial persistence in mycobacterial biofilms
Authors: Salini S. , Bhat Sinchana. G. , Nijisha M. , Ramachandran Reshma , Nikolas Nikhil , Kurthkoti Krishna
Published: October 2022

The complex cellular architecture and the microenvironments within the biofilm give rise to a population that is both physiologically and genetically heterogeneous. Transcriptome analysis ofMycobacterium smegmatisin biofilm culture and its transition phase into planktonic growth was performed to identify the genetic basis of heterogeneity in the biofilm. While there was an increase in the expression of mycobacterial mutasome consisting ofdnaE2, imuA, andimuBin the biofilm, the mutation burden was less compared to the planktonic culture. Deletion ofdnaE2causes lower mutation frequency and bacterial fitness in comparison to the parental strain in biofilm culture. The expression ofdnaE2contributes to a slower bacterial growth rate, potentially promoting persister formation. Our study uncovers the multiple benefits ofdnaE2expression in biofilm such as increasing genetic diversity and reducing growth rate; both of which are necessary for mycobacterial survival and adaptation.
Regulation of anterior neurectoderm specification and differentiation by BMP signaling in ascidians
Authors: Roure Agnès , Chowdhury Rafath , Darras Sébastien
Published: October 2022

Three palps make the most anterior structure of the ascidian larva. These ectodermal derivatives have both a sensory and adhesive functions essential for metamorphosis. They derive from the anterior neural border and their formation is regulated by signaling pathways such as FGF and Wnt. Since they also share gene expression profiles with vertebrate anterior neural tissue and cranial placodes, their study should shed light on the emergence of the unique vertebrate telencephalon. Here, we show that BMP signaling regulates two phases of palps formation inCiona intestinalis. During gastrula stages, the anterior neural border marked byFoxcis specified in a domain of inactive BMP signaling, and activating BMP prevented its formation. Later on, inhibiting BMP led to the formation of a single large palp, most likely of dorsal identity. Our results indicate that BMP signaling regulates papillavsinter-papilla fate decision within the palps forming region. Finally, we showed that modulating BMP signaling led to similar palps phenotypes in another ascidian speciesPhallusia mammillata. This led us to screen transcriptomic data and identify novel palps markers. Collectively, we provide a better molecular description of palps formation in ascidians that will be instrumental for comparative studies within ascidians and between ascidians and other chordates.
High performance genetically-encoded green fluorescent biosensors for intracellular L-lactate
Authors: Le Giang N. T. , Hario Saaya , Takahashi-Yamashiro Kei , Li Selene , Drobizhev Mikhail , Nasu Yusuke , Campbell Robert E.
Published: October 2022

L-Lactate is a monocarboxylate produced during the process of cellular glycolysis and has long been generally considered a waste product. However, studies in recent decades have provided new perspectives on the physiological roles of L-lactate as a major energy substrate and a signaling molecule. To enable further investigations of the physiological roles of L-lactate, we have developed a series of high-performance (ΔF/F= 15 to 30in vitro), intensiometric, genetically-encoded green fluorescent protein (GFP)-based intracellular L-lactate biosensors with a range of affinities. We evaluated the performance of these biosensors byin vitroand live-cell characterization and demonstrated the utility with imaging applications in several cell lines.
Stabilizing ferroelectricity in alkaline-earth-metal-based perovskites (ABO3) via A- (Ca2+/Sr2+/Ba2+) and B-site (Ti4+) cationic radius ratio (RA
/RB
)
Authors: Tripathi Anuvrat , Dubey Digvijay Nath , Kumar Harsh , Tripathi Saurabh
Published: October 2022

Various distortion parameters for alkaline-earth-metal-based perovskites (A
2+
B
4+O3) have been analyzed as a function of A- and B-site cationic radii R

A
and R

B
. The observed octahedral rotations and their associated mode amplitudes have shown an increasing trend with larger B-site cations, while a decreasing trend has been observed with larger A-site cations. Moreover, the analysis demonstrates that for incipient ferroelectrics like CaTiO3 and SrTiO3, having respective space groups Pnma (a
−
0
b
+
0
a
−
0) and Pm
3
m (a
0
0
a
0
0
a
0
0), ferroelectric displacements are achieved via cation manipulation, which is governed by the R

A
/R

B
parameter. The increase in R

A
/R

B
through substitutions on the A site may suppress octahedral rotations as well as A-site anti-polar displacements in CaTiO3 and can consequently lead to a ferroelectrically distorted BaTiO3-like P4mm (a
0
0
a
0
0
c
0
+) phase via a cubic phase of SrTiO3, which has an intermediate R

A
/R

B
parameter. These results have been further corroborated by the calculated amplitudes of various frozen phonon modes associated with the cubic Pm
3
m Brillouin zone, responsible for symmetry breaking to tilt-oriented non-ferroelectric Pnma and ferroelectric P4mm phases.
Efficient data reduction for time-of-flight neutron scattering experiments on single crystals
Authors: Savici Andrei T. , Gigg Martyn A. , Arnold Owen , Tolchenov Roman , Whitfield Ross E. , Hahn Steven E. , Zhou Wenduo , Zaliznyak Igor A.
Published: October 2022

Event-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.
Synthesis and crystal structure of 2-chloro-1-(3-hydroxyphenyl)ethanone
Authors: Priyanka Prabhakar , Jayanna Bidarur K. , Vinaya  , Shankara Prasad Holehundi J. , Divakara Thayamma R. , Yathirajan Hemmige S. , Parkin Sean
Published: October 2022

The structure of 2-chloro-1-(3-hydroxyphenyl)ethanone, C8H7ClO2, an α-haloketone is described. The molecule is planar (r.m.s. deviation = 0.0164 Å) and in the crystal, inversion-symmetric dimers are formed as a result of pairs of strong O—H...O and weak C—H...O hydrogen bonds. A brief comparison is made with structurally related compounds deposited in the CSD. In addition, the synthesis and some spectroscopic details are presented.
Synthesis, crystal structure and Hirshfeld surface analysis of catena-poly[[bis(semicarbazide-κ2
N,O)copper(II)]-μ-sulfato-κ2
O:O′]
Authors: Tadjieva Galiya , Ibragimov Aziz B. , Yakubov Yuldash , Ibragimov Bakhtiyar T. , Ashurov Jamshid M.
Published: October 2022

The title polymer, [Cu(SO4)(CH5N3O)2]
n
, has been synthesized from aqueous solutions of CuSO4 and semicarbazide. In the crystal structure, the CuII atoms are chelated by two neutral semicarbazide molecules through the oxygen atom and a nitrogen atom of the amino group. The remaining two positions of the Jahn–Teller-distorted octahedral coordination sphere are occupied by oxygen atoms of two sulfate anions in the axial positions. The coordination bonds of the latter associate the polyhedra into polymeric chains running parallel to the c axis. There is a weak intramolecular hydrogen bond between the N—H group and an oxygen atom of the SO4
2– anion. Thirteen relatively weak intermolecular hydrogen-bonding interactions link the chains into a three-dimensional network. Hirshfeld surface analysis revealed that 64.7% of the intermolecular interactions are from O...H/H...O contacts and 20.1% from H...H contacts. Other interactions such as N...H/H...N or C...H/H...C contribute less to the crystal packing.
Crystal structure of the cubic double-perovskite Sr2Cr0.84Ni0.09Os1.07O6
Authors: Chen Jie , Tsujimoto Yoshihiro , Belik Alexei A. , Yamaura Kazunari , Matsushita Yoshitaka
Published: October 2022

The crystal structure of the cubic double-perovskite Sr2Cr0.84Ni0.09Os1.07O6, grown at high pressure, was solved using intensity data measured at 113 K. The Os site was modelled with a partial Ni occupancy, and the Cr site was modelled with both Os and Ni partial occupancy. The refined structure shows that this cubic form is stable at 113 K.
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking
Authors: Trewhella Jill , Vachette Patrice , Bierma Jan , Blanchet Clement , Brookes Emre , Chakravarthy Srinivas , Chatzimagas Leonie , Cleveland Thomas E. , Cowieson Nathan , Crossett Ben , Duff Anthony P. , Franke Daniel , Gabel Frank , Gillilan Richard E. , Graewert Melissa , Grishaev Alexander , Guss J. Mitchell , Hammel Michal , Hopkins Jesse , Huang Qingqui , Hub Jochen S. , Hura Greg L. , Irving Thomas C. , Jeffries Cy Michael , Jeong Cheol , Kirby Nigel , Krueger Susan , Martel Anne , Matsui Tsutomu , Li Na , Pérez Javier , Porcar Lionel , Prangé Thierry , Rajkovic Ivan , Rocco Mattia , Rosenberg Daniel J. , Ryan Timothy M. , Seifert Soenke , Sekiguchi Hiroshi , Svergun Dmitri , Teixeira Susana , Thureau Aurelien , Weiss Thomas M. , Whitten Andrew E. , Wood Kathleen , Zuo Xiaobing
Published: October 2022

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å−1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to <0.5 Å−1, but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H2O and in D2O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å−1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.
Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans
Authors: Martins Marcele P. , Morais Mariana A. B. , Persinoti Gabriela F. , Galinari Rafael H. , Yu Li , Yoshimi Yoshihisa , Passos Nunes Fernanda B. , Lima Tatiani B. , Barbieri Shayla F. , Silveira Joana L. M. , Lombard Vincent , Terrapon Nicolas , Dupree Paul , Henrissat Bernard , Murakami Mário T.
Published: October 2022

Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-β-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-β-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing β6–α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the −1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.