bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural correlates of extinction in a rat model of appetitive Pavlovian conditioning
Authors: Brown Alexa , Villaruel Franz R. , Chaudhri Nadia
Published: October 2022

Extinction is a fundamental form of inhibitory learning that is important for adapting to changing environmental contingencies. While numerous studies have investigated the neural correlates of extinction using Pavlovian fear conditioning and appetitive operant reward-seeking procedures, less is known about the neural circuitry mediating the extinction of appetitive Pavlovian conditioned responding. Here, we aimed to generate an extensive brain activation map of extinction learning in a rat model of appetitive Pavlovian conditioning. Male Long-Evans rats were trained to associate a conditioned stimulus (CS; 20 s white noise) with the delivery of a 10% sucrose unconditioned stimulus (US; 0.3 ml/CS) to a fluid port. Control groups also received CS presentations, but sucrose was delivered either during the inter-trial interval or in the home-cage. After conditioning, 1 or 6 extinction sessions were conducted in which the CS was presented but sucrose was withheld. We performed Fos immunohistochemistry and network connectivity analyses on a set of cortical, striatal, thalamic, and amygdalar brain regions. Neural activity in the prelimbic cortex, ventral orbitofrontal cortex, nucleus accumbens core, and paraventricular nucleus of the thalamus was greater during recall relative to extinction. Conversely, prolonged extinction following 6 sessions induced increased neural activity in the infralimbic cortex, medial orbitofrontal cortex, and nucleus accumbens shell compared to home-cage controls. All these structures were similarly recruited during recall on the first extinction session. These findings provide novel evidence for the contribution of brain areas and neural networks that are differentially involved in the recall versus extinction of appetitive Pavlovian conditioned responding.
QUAS-R: Glutamine (Q) Uptake Assay with Single cell Resolution reveals metabolic heterogeneity with immune populations
Authors: Pelgrom Leonard , Davis Gavin , O’Shoughnessy Simon , Van Kasteren Sander , Finlay David , Sinclair Linda
Published: October 2022

System level analysis of single cell data is rapidly transforming the field of immunometabolism. However, metabolic profiling of single cells and small populations by flow and mass cytometry is extremely limited by the availability of specific reagents such as antibodies and fluorescently nutrient analogues. Given the competitive demand for nutrients in pathogenic microenvironments including sites of infection, tumours and autoinflammation, there is a need to understand how and when immune cells access these nutrients. Fluorescent-tagging of nutrients is one approach to study nutrient transport but is extremely limited in its usefulness as tagging usually changes the transport characteristics and transporter specificity of the nutrient. Herein, we developed a completely new approach for single cell analysis of nutrient uptake where a fluorophore is attached to a functionalized amino acid after it has been transported across the plasma membrane and is within the cell. This in-cell biorthogonal labelling ensures that bona fide transport has been measured. System ASC transporter SLC1A5/ASCT2 transports multiple amino acids, most notably the crucial fuel glutamine, and has essential roles in supporting immune metabolism, signalling and function. This flow cytometry assay allows for rapid, sensitive, and quantitative measurement of SLC1A5-mediated uptake, which we used to interrogate the transport capacity of the complex immune subpopulations within the thymus, at a single cell resolution previously “unreachable”. Taken together, our findings provide an easy procedure to assess which cells support their function via SLC1A5 mediated uptake of amino acids in a sensitive single cell assay. This assay is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.
Heritage of ancient cultures supports conservation: a continent-wide perspective from the Eurasian steppes
Authors: Deák Balázs , Bede Ádám , Rádai Zoltán , Dembicz Iwona , Apostolova Iva , Batáry Péter , Gallé Róbert , Tóth Csaba Albert , Dózsai József , Moysiyenko Ivan I. , Sudnik-Wójcikowska Barbara , Nekhrizov Georgi , Lisetskii Fedor N. , Buryak Zhanna A. , Kis Szabolcs , Borza Sándor , Godó Laura , Bragina Tatyana M. , Smelansky Ilya , Molnár Ábel , Bán Miklós , Báthori Ferenc , Árgay Zoltán , Dani János , Valkó Orsolya
Published: October 2022

Civilisations including ancient ones, have shaped the global ecosystems in many ways through a co-evolution of landscapes and humans. However, the cultural legacies of ancient and lost civilisations are seldom considered in conservation. Here using a continental-scale dataset containing over 1,000 data records on the localities, land cover, protection status and cultural values related to ancient steppic burial mounds (so-called ‘kurgans’), we evaluated how these iconic and widespread landmarks can contribute to grassland conservation in the Eurasian steppes, which is one of the most endangered biomes on Earth. By using Bayesian logistic generalized regressions and proportional odds logistic regressions, we aimed to reveal the potential of mounds in preserving grasslands considering landscapes with different levels of land use transformation. We also compared the conservation potential of mounds situated inside and outside protected areas and assessed whether the presence of cultural, historical or spiritual values support the maintenance of grasslands on them. We revealed that kurgans have enormous importance in preserving grasslands in transformed landscapes outside protected areas, where they can act as habitat islands, and provide an additional pillar for conservation by contributing to habitat conservation and improvement of habitat connectivity. We found that besides their steep slopes hindering ploughing, the existence of cultural, historical or religious values could almost double the chance for grassland occurrence on kurgans due to the related extensive land use and the respect of local communities. As the estimated number of steppic mounds is about 600,000 and also similar historical features exist in all continents, our results can be upscaled to a global level. Our results also suggest that an integrative socio-ecological approach in conservation might support the positive synergistic effects of conservational, landscape and cultural values.
ZNF251haploinsufficiency confers PARP inhibitors resistance inBRCA1-mutated cancer cells through activation of homologous recombination
Authors: Li Huan , Chatla Srinivas , Liu Xiaolei , Tian Zhen , Vekariya Umeshkumar , Wang Peng , Kim Dongwook , Octaviani Stacia , Lian Zhaorui , Morton George , Feng Zijie , Yang Dan , Sullivan-Reed Katherine , Childers Wayne , Yu Xiang , Chitrala Kumaraswamy Naidu , Madzo Jozef , Skorski Tomasz , Huang Jian
Published: October 2022

Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a promising new class of agents that have demonstrated efficacy in treating various cancers, particularly those withBRCA1/2mutations. Cancer-associatedBRCA1/2mutations disrupt DNA double-strand break (DSB) repair by homologous recombination (HR). PARP inhibitors (PARPis) have been used to trigger synthetic lethality inBRCA1/2-mutated cancer cells by promoting the accumulation of toxic DSBs. Unfortunately, resistance to PARPis is common and can occur through multiple mechanisms, including the restoration of HR and/or stabilization of replication forks. To gain a better understanding of the mechanisms underlying PARPis resistance, we conducted an unbiased CRISPR-pooled genome-wide library screen to identify new genes whose deficiency confers resistance to the PARPi olaparib. Our research revealed that haploinsufficiency of theZNF251gene, which encodes zinc finger protein 251, is associated with resistance to PARPis in various breast and ovarian cancer cell lines carryingBRCA1mutations. Mechanistically, we discovered thatZNF251haploinsufficiency leads to stimulation of RAD51-mediated HR repair of DSBs in olaparib-treatedBRCA1-mutated cancer cells. Moreover, we demonstrated that a RAD51 inhibitor reversed PARPi resistance inZNF251haploinsufficient cancer cells harboringBRCA1mutations. Our findings provide important insights into the mechanisms underlying PARPis resistance by highlighting the role of RAD51 in this phenomenon.
The SARS-CoV-2 mutation landscape is shaped before replication starts
Authors: Masone Diego , Alvarez Maria Soledad , Polo Luis Mariano
Published: October 2022

Mutation landscapes and signatures have been thoroughly studied in SARS-CoV-2. Here, we analyse those patterns and link their changes to the viral replication niche. Surprisingly, those patterns look to be also modified after vaccination. Hence, by deductive reasoning we identify the steps of the coronavirus infection cycle in which those mutations initiate.
Antimicrobial Resistance, Genomic, and Public Health Insights into Enterococcus spp. from Australian Cattle
Authors: Sahibzada Shafi , Abraham Rebecca , Lee Terence , Jordan David , McMillan Kate , Mellor Glen , Duffy Lesley , O’Dea Mark , Abraham Sam , Barlow Robert
Published: October 2022

Enterococci are opportunistic, potentially life-threatening pathogens of humans that are difficult to manage due to antimicrobial resistance. Historically, enterococci entering the food-chain through livestock have been viewed as a likely source of antimicrobial resistance in humans. Australian human-derived clinical enterococci have a propensity to be resistant to multiple classes of antimicrobials including vancomycin. Recent Australian studies involving pigs and chicken have virtually excluded these species as reservoirs of infection for resistant enterococci in humans. However, the Australian bovine population has not been similarly assessed. This study investigates the antimicrobial resistance profiles of enterococci from Australian cattle and the phylogenetic relationship between E. faecium isolated from cattle and human sepsis cases. Minimum inhibitory concentration assays were performed for E. faecium (n=343), E. faecalis (n=92), and E. hirae (n=284) against a panel of 15 antimicrobials. The majority of isolates were sensitive to all tested antimicrobials. Erythromycin resistance was most prevalent for E. faecium isolates (18.7%), daptomycin for E. faecalis (12.1%) and tetracycline for E. hirae (13.3%). Phenotypically, 1 E. faecalis was resistant to vancomycin and 9 were resistant to linezolid (E. faecium n=4, E. faecalis n=2, E. hirae n=3) but this was not confirmed with any know genotype. A subset of 67 E. faecium isolates selected for comparative phylogenetic analysis revealed that bovine isolates clustered with other livestock-derived and van-negative human isolates. In conclusion, there is a low prevalence of antimicrobial resistance amongst enterococci from Australian cattle which are unlikely to be precursor strains to vancomycin-resistant strains currently circulating in Australian hospitals.

Importance

Enterococci resistant to critically important antimicrobials such as vancomycin and linezolid are difficult to manage in health care settings. Historically, there has been the belief that livestock can act as a reservoir of resistance for human infections. Previous studies in poultry and pork have demonstrated that isolates derived from these livestock are unlikely to be precursor strains for currently circulating vancomycin resistant-Enterococci causing infection in humans. To date, there has been no study looking at the genetic similarity of bovine derived Enterococci and the relationship to human pathogenic strains. In this study we performed phenotypic and genotypic characterization of bovine derived Enterococci along with comparative phylogenetic analysis with other livestock derived and human sepsis derived E. faecium isolates. We found that while non-vancomycin resistant strain sharing occurs between hosts, cattle are unlikely to be precursor strains for vancomycin resistant human E. faecium infections.
COVID-19 vaccine antibody response is associated with side-effects, chronic health conditions, and vaccine type in a large Northern California cohort
Authors: Solomon Olivia , Adams Cameron , Horton Mary , Wong Marcus P. , Meas Michelle , Shao Xiaorong , Fedrigo Indro , Hernandez Samantha , Quach Hong L. , Quach Diana L. , Barcellos Anna L. , Coloma Josefina , Busch Michael , Harris Eva , Barcellos Lisa F.
Published: October 2022

As vaccines have become available for COVID-19, it is important to understand factors that may impact response. The objective of this study is to describe vaccine response in a well-characterized Northern California cohort, including differences in side-effects and antibody response by vaccine type, sex, and age, as well as describe responses in subjects with pre-existing health conditions that are known risk factors for more severe COVID-19 infection. From July 2020 to March 2021, ∼5,500 adults from the East Bay Area in Northern California were followed as part of a longitudinal cohort study. Comprehensive questionnaire data and biospecimens for COVID-19 antibody testing were collected at multiple time-points. All subjects were at least 18 years of age and members of the East-Bay COVID-19 cohort who answered questionnaires related to vaccination status and side-effects at two time-points. Three vaccines, Moderna (2 doses), Pfizer-BioNTech (2 doses), and Johnson & Johnson (single dose), were examined as exposures. Additionally, pre-existing health conditions were assessed. The main outcomes of interest were anti-SARS-CoV-2 Spike antibody response (measured by S/C ratio in the Ortho VITROS assay) and self-reporting of 11 potential vaccine side effects. When comparing both doses of the Moderna vaccine to respective doses of Pfizer-BioNTech, participants receiving the Moderna vaccine had higher odds of many reported side-effects. The same was true comparing the single-dose Johnson & Johnson vaccine to dose 2 of the Pfizer-BioNTech vaccine. The antibody S/C ratio also increased with each additional side-effect after the second dose. S/C ratios after vaccination were lower in participants aged 65 and older, and higher in females. At all vaccination timepoints, Moderna vaccine recipients had a higher S/C ratio. Individuals who were fully vaccinated with Pfizer-BioNTech had a 72.4% lower S/C ratio compared to those who were fully vaccinated with Moderna. Subjects with asthma, diabetes, and cardiovascular disease all demonstrated more than a 20% decrease in S/C ratio. In support of previous findings, we show that antibody response to the Moderna vaccine is higher than the Pfizer-BioNTech vaccine. We also observed that antibody response was associated with side-effects, and participants with a history of asthma, diabetes, and cardiovascular disease had lower antibody responses. This information is important to consider as further vaccines are recommended.
HIV positive patients on HAART continue to have a decline in renal function irrespective of Tenofovir usage: A 2-year cohort from an Indian tertiary care centre
Authors: Joshi Kavita S. , Jadhao Viplove F. , Gujarathi Rushabh Y. , Churiwala Widhi , Natu Anuya A.
Published: October 2022

Context

HIV patients may undergo renal damage due to disease or nephrotoxic drugs. Tenofovir has been associated with the development of renal impairment.

Aims

To study and compare trends in Creatinine Clearance (CrCl) and estimated Glomerular Filtration Rate (eGFR) in patients on Highly Active Antiretroviral Therapy (HAART) and to compare the same between patients on Tenofovir and non-Tenofovir based regimens.

Methods

A cross-sectional study was conducted. We followed 244 patients for a period of 2 years. The demographic, clinical, and laboratory parameters of the patients were recorded at baseline, one year of therapy, and two years of therapy. The data was analyzed by dividing patients into Tenofovir and non-Tenofovir based groups. Statistical analysis used the Chi-square test, paired and unpaired t-tests, and Fischer’s exact test.

Results

The mean BUN and serum creatinine in both groups were comparable at the start of the therapy. The decline in CrCl and eGFR in all patients on HAART for two years was statistically significant, irrespective of Tenofovir usage. The mean fall in eGFR in the Tenofovir group was 12.4 mL/min/1.73 m2 and in the non-Tenofovir group, 9 mL/min/1.73 m2, though the differences between eGFR and CrCl were not significant between the two groups at any point.

Conclusions

Even though HAART usage has been said to slow the decline in kidney function in PLHIV, patients who receive HAART still show a statistically significant decline in renal function parameters, akin to the observations of other such studies in low-resource settings.
Utilization of Emergency Care by an East African Refugee Community Compared to Local Residents in Central Minnesota: A Cross-Sectional Study
Authors: Hughes-Scalise Abby , Ayanle Mohamed , Dakoji Srikanth
Published: October 2022

Background

Previous studies on emergency service utilization by refugees have been mixed, with some showing overuse and others showing underuse relative to host populations. Much of the previous literature focuses on refugees by continent of origin, which may mask important differences within immigrant groups. Limited research has investigated emergency medicine utilization for East African refugees in the United States.

Methods

The current study investigated differences in ED service utilization for East African refugees compared to local residents at an Emergency Trauma Center (Level 2) in Central Minnesota. From a convenience sample of 48 East African refugees and 116 local residents that presented to an emergency department (ED) in Central Minnesota, survey data was collected on self-reported reasons for presenting to ED; chart review data was collected on care received at the emergency department and discharge diagnoses.

Results

Logistic regressions showed that refugees were significantly (p < .05) more likely than local residents to self-report difficulties with navigating the primary care settings as a reason for presenting to the ED, and less likely to report needing specialized care. Refugees were also significantly less likely than local residents to call their primary care provider/clinic before presenting to the ED. During the ED visit, refugees were significantly more likely than local residents to receive symptomatic care and less likely to receive advanced imaging.

Conclusion

We hope these results spur additional research on this unique population, particularly related to health literacy and health equity in an emergency medicine setting for East African refugees continuing to migrate to the United States at high rates.
Cross-modal interactions at the audiovisual cocktail-party revealed by behavior, ERPs, and neural oscillations
Authors: Klatt Laura-Isabelle , Begau Alexandra , Schneider Daniel , Wascher Edmund , Getzmann Stephan
Published: October 2022

Theories of attention argue that objects are the units of attentional selection. In real-word environments such objects can contain visual and auditory features. To understand how mechanisms of selective attention operate in multisensory environments, we created an audiovisual cocktail-party situation, in which two speakers (left and right of fixation) simultaneously articulated brief numerals. In three separate blocks, informative auditory speech was presented (a) alone or paired with (b) congruent or (c) uninformative visual speech. In all blocks, subjects localized a pre-defined numeral. While audiovisual-congruent and uninformative speech improved response times and speed of information uptake according to diffusion modeling, an ERP analysis revealed that this did not coincide with enhanced attentional engagement. Yet, consistent with object-based attentional selection, the deployment of auditory spatial attention (N2ac) was accompanied by visuo-spatial attentional orienting (N2pc) irrespective of the informational content of visual speech. Notably, an N2pc component was absent in the auditory-only condition, demonstrating that a sound-induced shift of visuo-spatial attention relies on the availability of audio-visual features evolving coherently in time. Additional analyses revealed cross-modal interactions in working memory and modulations of cognitive control. The preregistered methods and hypotheses of this study can be found athttps://osf.io/vh38g.
Changes in a new type of genomic accordion may open the pallets to increased monkeypox transmissibility
Authors: Monzón Sara , Varona Sarai , Negredo Anabel , Patiño-Galindo Juan Angel , Vidal-Freire Santiago , Zaballos Angel , Orviz Eva , Ayerdi Oskar , Muñoz-García Ana , Delgado-Iribarren Alberto , Estrada Vicente , García Cristina , Molero Francisca , Sánchez Patricia , Torres Montserrat , Vázquez Ana , Galán Juan-Carlos , Torres Ignacio , Causse del Río Manuel , Merino Laura , López Marcos , Galar Alicia , Cardeñoso Laura , Gutiérrez Almudena , Loras Cristina , Escribano Isabel , Alvarez-Argüelles Marta Elena , del Río Leticia , Simón María , Meléndez MªAngeles , Camacho Juan , Herrero Laura , Sancho Pilar Jiménez , Navarro-Rico Maria Luisa , Kuhn Jens H. , Sanchez-Lockhart Mariano , Paola Nicholas Di , Kugelman Jeffrey R. , Giannetti Elaina , Guerra Susana , García-Sastre Adolfo , Palacios Gustavo , Cuesta Isabel , Sánchez-Seco Maripaz P.
Published: October 2022

The currently expanding monkeypox epidemic is caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. In contrast to monkeypox cases caused by clade I and subclade IIa MPXV, the prognosis of current cases is generally favorable, but person-to-person transmission is much more efficient. MPXV evolution is driven by selective pressure from hosts and loss of virus–host interacting genes. However, there is no satisfactory genetic explanation using single-nucleotide polymorphisms (SNPs) for the observed increased MPXV transmissibility. We hypothesized that key genomic changes may occur in the genome’s low-complexity regions (LCRs), which are highly challenging to sequence and have been dismissed as uninformative. Using a combination of highly sensitive techniques, we determined a first high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This effort revealed significant variation in short-tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of SNPs and that LCRs are not randomly distributed.In silicoanalyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs) 153, 204, and 208 could be affected in a manner consistent with the established “genomic accordion” evolutionary strategies of orthopoxviruses. Consequently, we posit that genomic studies focusing on phenotypic MPXV clade-/subclade-/lineage-/strain differences should change their focus to the study of LCR variability instead of SNP variability.
Characterization of the Doublesex/MAB-3 transcription factor DMD-9 in Caenorhabditis elegans
Authors: Godini Rasoul , Pocock Roger
Published: October 2022

DMD-9 is a Caenorhabditis elegans Doublesex/MAB-3 Domain transcription factor of unknown function. Single-cell transcriptomics revealed that dmd-9 is highly expressed in specific head sensory neurons, with lower levels detected in non-neuronal tissues (uterine cells and spermatheca). Here, we characterized endogenous dmd-9 expression and function in hermaphrodites and males to identify potential sexually dimorphic roles. In addition, we dissected the trans- and cis-regulatory mechanisms that control DMD-9 expression in neurons. Our results show that of the 22 DMD-9-expressing neuronal reporters we analyzed, only the neuropeptide-encoding flp-19 gene is cell-autonomously regulated by DMD-9. Further, we did not identify defects in behaviors mediated by DMD-9 expressing neurons in dmd-9 mutants. We found that dmd-9 expression in neurons is regulated by four neuronal fate regulatory TFs: ETS-5, EGL-13, CHE-1, and TTX-1. In conclusion, our study characterized the DMD-9 expression pattern and regulatory logic for its control. We found that, as with other DMD TFs, DMD-9 likely acts redundantly to control neuronal development and function.
Angiotensin II Type 2 Receptor Potentiates Skeletal Muscle Satellite Cell Differentiation via the GSK3β/β-catenin Pathway
Authors: Lott C Seth , Chandrasekar Bysani , Delafontaine Patrice , Yoshida Tadashi
Published: October 2022

Patients with advanced congestive heart failure (CHF) or chronic kidney disease (CKD) often have increased systemic angiotensin II (Ang II) levels and cachexia. We previously demonstrated that Ang II infusion in rodents results in skeletal muscle wasting and reduced muscle regenerative potential via Ang II type 1 receptor (AT1R) signaling, potentially contributing to cachexia in CHF and CKD. Contrary to AT1R signaling, we found that signaling via Ang II type 2 receptor (AT2R) potentiates skeletal muscle satellite cell (SC) differentiation and muscle regenerative potential. However, mechanisms whereby AT2R regulates SC differentiation and cachexia development remain unknown. In this study, we found that GSK3β activity was significantly suppressed during SC differentiation, whereas it was retained in SCs with AT2R knockdown. AT2R knockdown leads to higher GSK3β and decreased β-catenin activities bothin vitroandin vivo. Treatment with GSK3β inhibitor BIO restored β-catenin activity and differentiation capacity of SCs with AT2R knockdown. Conversely, transgenic overexpression of AT2R in SCs inhibited GSK3β, associated with increased β-catenin activity and SC myogenic capacity bothin vitroandin vivo. Interestingly, AT2R expression in undifferentiated SCs was regulated post-transcriptionally. An increase in systemic Ang II blunted AT2R induction during muscle regeneration. However, overexpression of AT2R restored AT2R levels and myogenesisin vivo. Together, these data suggest that the AT2R/GSK3β/β- catenin signaling pathway could serve as a potential therapeutic target to promote muscle regenerative capacity in chronic disease conditions characterized by heightened activation of the renin-angiotensin system, such as CHF and CKD.
THE ASSOCIATION OF CD47 WITH INTEGRIN Mac-1 REGULATES MACROPHAGE RESPONSES BY STABILIZING THE EXTENDED INTEGRIN CONFORMATION
Authors: Podolnikova Nataly P. , Key Shundene , Wang Xu , Ugarova Tatiana P.
Published: October 2022

CD47 is a ubiquitously expressed cell surface integrin-associated protein. Recently, we have demonstrated that integrin Mac-1 (αMβ2, CD11b/CD18, CR3), the major adhesion receptor on the surface of myeloid cells, can be coprecipitated with CD47. However, the molecular basis for the CD47-Mac-1 interaction and its functional consequences remain unclear. Here, we demonstrated that CD47 regulates macrophage functions directly interacting with Mac-1. In particular, adhesion, spreading, migration, phagocytosis, and fusion of CD47-deficient macrophages were significantly decreased. The functional link between CD47 and Mac-1 was validated by co-immunoprecipitation analysis using various Mac-1-expressing cells. In HEK293 cells expressing individual αM and β2 integrin subunits, CD47 has been found to bind both subunits. Interestingly, the amount of CD47 recovered with the free β2 subunit was higher than in the complex with the whole integrin. Furthermore, activating Mac-1-expressing HEK293 cells with PMA, Mn2+, and activating antibody increased CD47 in complex with Mac-1, suggesting greater stability of the complex with integrin in the extended conformation. Notably, on the surface of cells lacking CD47, fewer Mac-1 molecules could convert into an extended conformation in response to activation. The binding site in CD47 for Mac-1 was identified in its constituent IgV domain. The complementary binding sites for CD47 in Mac-1 were localized in integrin epidermal growth factor-like domains 3 and 4 of the β2 and calf-1 and calf-2 domains of the α subunits. These results indicate that Mac-1 forms a lateral complex with CD47, which regulates essential macrophage functions by stabilizing the extended integrin conformation.
A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil
Authors: Nicolas Alexa M. , Sieradzki Ella T. , Pett-Ridge Jennifer , Banfield Jillian F. , Taga Michiko E. , Firestone Mary K. , Blazewicz Steven J.
Published: October 2022

Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigated lineage-specific virus-host dynamics in grassland soil following “wet-up”, when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicated that dry soil held a diverse but low biomass reservoir of virions, of which only a subset thrived following wet-up. Viral richness decreased by 50% within 24 h post wet-up, while viral biomass increased four-fold within one week. Counter to recent hypotheses suggesting temperate viruses predominate in soil, our evidence indicates that wet-up is dominated by viruses in lytic cycles. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2efflux following wet-up of seasonally dry soils.
Re-evaluation and Re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 20%
Authors: Bartolomaeus Tobias , Hentschel Julia , Jamra Rami Abou , Popp Bernt
Published: October 2022

Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases.

We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations. Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis.

In 30/152 (20%) families, we identified a clinically relevant change. Thirteen previously reported (likely) pathogenic variants were re-classified as VUS/benign. In three cases, the gene-disease association (TSEN15, NAPB, and FAR1) validity was judged as limited. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues.

Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
In-depth investigations of size and occupancies in cobalt ferrite nanoparticles by joint Rietveld refinements of X-ray and neutron powder diffraction data
Authors: Henry Killian , Ahlburg Jakob Voldum , Andersen Henrik L. , Granados-Miralles Cecilia , Stingaciu Marian , Saura-Múzquiz Matilde , Christensen Mogens
Published: October 2022

Powder X-ray diffraction (PXRD) and neutron powder diffraction (NPD) have been used to investigate the crystal structure of CoFe2O4 nanoparticles prepared via different hydrothermal synthesis routes, with particular attention given to accurately determining the spinel inversion degrees. The study is divided into four parts. In the first part, the investigations focus on the influence of using different diffraction pattern combinations (NPD, Cu-source PXRD and Co-source PXRD) for the structural modelling. It is found that combining PXRD data from a Co source with NPD data offers a robust structural model. The second part of the study evaluates the reproducibility of the employed multipattern Rietveld refinement procedure using different data sets collected on the same sample, as well as on equivalently prepared samples. The refinement procedure gives reproducible results and reveals that the synthesis method is likewise reproducible since only minor differences are noted between the samples. The third part focuses on the structural consequences of (i) the employed heating rate (achieved using three different hydrothermal reactor types) and (ii) changing the cobalt salt in the precursors [aqueous salt solutions of Co(CH3COOH)2, Co(NO3)2 and CoCl2] in the synthesis. It is found that increasing the heating rate causes a change in the crystal structure (unit cell and crystallite sizes) while the Co/Fe occupancy and magnetic parameters remain similar in all cases. Also, changing the type of cobalt salt does not alter the final crystal/magnetic structure of the CoFe2O4 nanoparticles. The last part of this study is a consideration of the chemicals and parameters used in the synthesis of the different samples. All the presented samples exhibit a similar crystal and magnetic structure, with only minor deviations. It is also evident that the refinement method used played a key role in the description of the sample.
Improvement of performance of the RC beams using the longitudinal spiral reinforcements
Authors: Labibzadeh Mojtaba , Bostan Shirin Farhad , Khajehdezfuly Amin
Published: October 2022

Purpose

This study aims to investigate the effects of using circular spirals as the longitudinal reinforcing bars on the performance of the concrete beams subjected to four-point bending load.

Design/methodology/approach

The effects of using circular spirals as the longitudinal reinforcing bars on the performance of the concrete beams subjected to four-point bending load are investigated in this study. Employing circular spirals as the main longitudinal reinforcement is a novel idea presented in this paper. In this regard, a finite element model of the beam with spiral longitudinal reinforcement was developed. After model verification, several configurations of concrete beams reinforced by longitudinal spirals were simulated under the four-point loading condition.

Findings

Obtained results showed that using the longitudinal spirals in place of the conventional longitudinal reinforcing bars can improve the bearing capacity of the concrete beam, but at the same time, increases its ductility unacceptably. In other words, the spirals reduce the initial stiffness of the beam significantly. To solve the problem, the authors decided to use the longitudinal spirals as the auxiliary bars added to the main conventional longitudinal bars in the beams. New gained results were satisfactory. By adding the longitudinal spirals to the conventional bars, not only the bearing capacity of the beam increases between 24% and 63%, but also the initial stiffness and ductility of the beam raises between 11%–29% and 3%–57%, respectively, in comparison to the corresponding beam reinforced with conventional longitudinal bars.

Originality/value

Employing circular spirals as the main longitudinal reinforcement is a novel idea presented in this paper.
The link and spillovers between clean energy and fossil fuels market: a systematic literature review
Authors: Xia Summer
Published: October 2022

Purpose

The global transition into clean energy demands a re-examination of the link between fossil fuels and clean energy markets. This paper aims to identify the key research areas about clean energy and fossil fuels and outlines emerging themes for future research.

Design/methodology/approach

This paper uses bibliographic mapping to identify the most influential publications among 500 articles published between 1991 and 2022 (as of March 2022). The first step is the identification of literature for inclusion and data cleaning. Next is producing a citation map using Bibliometrix for analysis and synthesis.

Findings

The research on clean energy and fossil fuels has developed into three areas by examining their dynamic causality, return/risk spillovers, and volatility spillovers. However, pr evious studies focus on the oil and clean energy market, and limited studies examine the market linkage. As a result, market linkage presents a challenge in front of energy transition into a green economy.

Originality/value

This paper makes a clear contribution to the literature by identifying the important existing and emerging research areas on the clean energy and fossil fuels market.
Mosque as a multi-functional public space destination: potential breathing space in dense urban fabrics of Hail City, Saudi Arabia
Authors: Alnaim Mohammed M. , Noaime Emad
Published: October 2022

Purpose

The general concept of public space in Saudi Arabia is relatively recent; it is the result of an attempt to modernize several conservative traditions and norms, as well as the ambitious vision of 2030, which reprioritized Saudi cities' public spaces by implementing a quality-of-life improvement program. This study aims to investigate the relationship between mosque location and surrounding urban context as a significant urban design issue in order to comprehend the potential for transforming such an element into a multifunctional public space destination in a dense urban fabric.

Design/methodology/approach

The study's objectives are divided into two areas: a spatial configuration analysis to examine the urban context and an urban analysis of the mosque site with a study area boundary of a 400-m buffer zone. Quantitative and qualitative methodologies were utilized; in addition, a user feedback survey was conducted in which several key insights were compiled, such as the importance of safety urban element factors, aesthetic elements and green areas in the built environment in making mosques places that are active public spaces.

Findings

The study’s main finding encourages governmental institutions to change their mindset from “open space around the mosque” to “the mosque as an element within public space,” which will have a significant impact on how the authors approach, improve and redevelop existing mosque locations. Several concepts were presented that should be reconsidered and redeveloped in order to align with the most recent sustainable urban design tools; the mosque to be overlooked as a community gathering place rather than just a place for religious rituals.

Research limitations/implications

This study is limited to sacred mosque sites primarily found in Islamic countries; it focuses on Saudi Arabian urban and planning practices in relation to sociocultural norms. The authors believe that increasing the number of study samples or broadening the scope of the study to include other Saudi regions or other Middle Eastern countries could yield new findings and insights.

Originality/value

The study offers a conceptual design model based on survey results and qualitative analysis and recommending strategies that planners, designers and policymakers can use to design successful mosque places and pedestrian-oriented developments.
Politics and PTSD: The case of Hong Kong BN(O) visa arrivals in the UK
Authors: Liang Mark Chih‐Wei
Published: October 2022

This article adopts an ethnographic perspective to present the mental health situation of arrivals from Hong Kong (HK) to the UK on the British National (Overseas) – BN(O) – visa. In the months after the 2019–2020 HK protests, Western and Chinese media announced the onset of a mental health crisis. I discuss the construction of this crisis in terms of post‐traumatic stress disorder (PTSD) and disaster mental health, which translate the role of trauma from the clinical sphere into a marker of a moral economy. I also argue that the UK and the People's Republic of China classify populations according to ontological structures of distress for political gain. In this way, they participate in ‘damage‐centred’ research, which regards BN(O) visa holders in the UK as victims without agency and subject to global players. By taking an anthropological stance on the debates surrounding this nascent immigrant group, I assert that PTSD is always political and that mental health integrates itself into larger goals Hongkongers have regarding their future educational, housing and employment prospects in the UK.
Impact of COVID‐19 inequalities on children: An intersectional analysis
Authors: Lemkow–Tovías Gabriel , Lemkow Louis , Cash‐Gibson Lucinda , Teixidó‐Compañó Ester , Benach Joan
Published: October 2022

Societal concerns about the effects of the COVID‐19 pandemic have largely focussed on the social groups most directly affected, such as the elderly and health workers. However, less focus has been placed on understanding the effects on other collectives, such as children. While children’s physical health appears to be less affected than the adult population, their mental health, learning and wellbeing is likely to have been significantly negatively affected during the pandemic due to the varying policy restrictions, such as withdrawal from face to face schooling, limited peer‐to‐peer interactions and mobility and increased exposure to the digital world amongst other things. Children from vulnerable social backgrounds, and especially girls, will be most negatively affected by the impact of COVID‐19, given their different intersecting realities and the power structures already negatively affecting them. To strengthen the understanding of the social determinants of the COVID‐19 crisis that unequally influence children’s health and wellbeing, this article presents a conceptual framework that considers the multiple axes of inequalities and power relations. This understanding can then be used to inform analyses and impact assessments, and in turn inform the development of effective and equitable mitigation strategies as well as assist to be better prepared for future pandemics.
Nonthermal pasteurization of pineapple juice: A review on the potential of achieving microbial safety and enzymatic stability
Authors: Shaik Lubna , Chakraborty Snehasis
Published: October 2022

Pineapple juice is preferred by consumers for its unique aroma and flavor that come from a set of amino acids, amines, phenolic compounds, and furanone. The juice is susceptible to spoilage, and a common practice is to pasteurize it at 70–95°C for 0.5–5 min. However, the characteristic flavors and phytochemicals are negatively influenced by the intense time–temperature treatment. To retain the thermosensitive compounds in the juice, some nonthermal technologies such as high‐pressure processing, pulsed electric field, pulsed light, ultrasound, and ultraviolet treatments have been explored. These techniques ensured microbial safety (5‐log reduction inE. coli,S. Typhimurium, orS. cerevisiae) while preserving a maximum ascorbic acid (84–99%) in the juice. The shelf life of these nonthermally treated juice varied between 14 days (UV treated at 7.5 mJ/cm2) and 6 months (clarified through microfiltration). Moreover, the inactivation of spoilage enzyme in the juice required a higher intensity. The present review discusses the potential of several nonthermal techniques employed for the pasteurization of pineapple juice. The pasteurization ability of the combined hurdle between mild thermal and nonthermal processing is also presented. The review also summarizes the target for pasteurization, the plan to design a nonthermal processing intensity, and the consumer perspective toward nonthermally treated pineapple juice. The techniques are compared on the common ground like safety, stability, and quality of the juice. This will help readers to select an appropriate nonthermal technology for pineapple juice production and design the intensity required to satisfy the manufacturers, retailers, and consumers.
Novel isochoric impregnation to develop high‐quality and nutritionally fortified plant materials (apples and sweet potatoes)
Authors: Bilbao‐Sainz Cristina , Chiou Bor‐Sen , Takeoka Gary , Williams Tina , Wood Delilah , Powell‐Palm Matthew J. , Rubinsky Boris , McHugh Tara
Published: October 2022

Isochoric impregnation was explored as a novel pressure‐assisted infusion technique to fortify plant materials with bioactive compounds. Apple and potato cylinders were impregnated with a sucrose solution containing 4% ascorbic acid (AA) while freezing under isochoric conditions. Isochoric impregnation resulted in greater infusion of AA compared to infusion at atmospheric pressure, which demonstrated the feasibility of this impregnation technology. Processing temperatures (–3°C and –5°C) and processing times (1, 3, and 5 h) significantly affected the AA infusion. The AA content values ranged from 446 to 516 mg/100 g for apples and 322 to 831 mg/100 g for sweet potatoes under isochoric conditions. For both plant materials, isochoric impregnation at –3°C did not cause major changes in texture and microstructure of the biological tissues. These results indicated that isochoric impregnation of solid foods could be a feasible technology for infusion of bioactive compounds without significantly altering their matrix.

Practical Application

The findings of this study showed that the use of isochoric impregnation as a fortification technique is a promising way to develop fresh‐like and value‐added products with improved nutrition during preservation at subfreezing temperatures.
Gestational diabetes mellitus in the COVID‐19 pandemic: A retrospective study from Hangzhou, China
Authors: Yin Binbin , Wu Kaiqi , Hu Lingwei , Zheng Wanlu , Zheng Yidan , Duan Xiuzhi , Zhu Bo
Published: October 2022

Aims

Our study aimed to investigate changes in the prevalence of gestational diabetes mellitus (GDM) in the COVID‐19 pandemic and postpandemic era and the risk of adverse pregnancy outcomes in pregnant women diagnosed with GDM during the blockade period.

Methods

First, we investigated changes in the prevalence of GDM and the population undergoing oral glucose tolerance tests (OGTT) after the COVID‐19 pandemic. We then collected clinical information from pregnant women diagnosed with GDM to explore the risk of adverse pregnancy outcomes in pregnant women with GDM during the COVID‐19 pandemic.

Results

After the COVID‐19 pandemic, the proportion of pregnant women in the total number of outpatient OGTT tests decreased yearly. The ratio was 81.30%, 79.71%, and 75.48% from 2019 to 2021, respectively, with the highest proportion of pregnant women in February 2020 (92.03%). The prevalence of GDM was higher in March 2020 compared to the same period in 2019. However, from 2019 to 2021, the prevalence decreased year by year with 21.46%, 19.81%, and 18.48%, respectively. The risk of adverse pregnancy outcomes for pregnant women diagnosed with GDM during the most severe period of the COVID‐19 pandemic did not differ from before the COVID‐19 pandemic.

Conclusions

After the COVID‐19 pandemic, the prevalence of GDM increased during the most severe period of the epidemic, but the overall prevalence of GDM decreased year by year. In addition, the pandemic did not change the risk of adverse pregnancy outcomes in pregnant women with GDM.